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PubMed1997

The concept of an evolved adaptation.

A Darwinian adaptation is an organism's feature that was functionally designed by the process of evolution by selection acting in nature in the past. Functional design rules out explanations of drift, incidental effect, phylogenetic legacy and mutation. Elucidation of the functional design of an adaptation entails an implicit reconstruction of the selection that made the adaptation. Darwinian adaptations and other individual traits may be currently adaptive, maladaptive or neutral. One relatively recent meaning of adaptation is inconsistent with the Darwinian conception of adaptation. The inconsistent meaning characterizes much research on humans and non-human species in behavioural ecology. Its focus is on equating Darwinian adaptation with current adaptiveness. Current adaptiveness is not an actual scientific prediction of a hypothesis about Darwinian adaptation. Some aspects of the discussion in the evolutionary literature surrounding the current adaptiveness view of adaptation are evaluated. Contrary to claims by some who advocate current adaptiveness, the environment of evolutionary adaptedness of humans and other organisms is scientifically knowable through discovery of the functional design of Darwinian adaptations.

Adaptation, Psychological↗

PubMed1994

Evolutionary algorithms and a fractal inverse problem.

Over the past 30 years, algorithms that model natural evolution have generated robust search methods. These so-called evolutionary algorithms have been successfully applied to a wide range of problems. This paper discusses two types of evolutionary algorithms and their application to a problem in shape representation. Genetic algorithms and evolutionary programming, although both based on evolutionary principles, each place different emphasis on what drives the evolutionary process. While genetic algorithms rely on mimicking specific genotypic transformations, evolutionary programming emphasizes phenotypic adaptation. Results presented show the success of evolutionary programming in solving an example of a fractal inverse problem, but indicate that a genetic algorithm is not as successful. Reasons for this disparity are discussed.

Algorithms↗

PubMed2000

Parasite adaptation to locally common host genotypes.

According to the Red Queen hypothesis--which states that interactions among species (such as hosts and parasites) lead to constant natural selection for adaptation and counter-adaptation--the disproportionate evolutionary success of parasites on common host genotypes leads to correlated selection for sexual reproduction and local adaptation by the parasite population. Here we determined whether local adaptation is due to disproportionate infection of common host genotypes, and, if so, whether infection of common host genotypes is due to commonness per se, or some other aspect of these genotypes. In a reciprocal cross-inoculation experiment parasites occupying the same geographical area (sympatric) infected locally common host genotypes significantly more often than rare host genotypes, whereas parasites occupying separate geographical areas (allopatric) showed no such significant difference. A mixed source of parasites (containing F1 hybrids) also showed no difference in infection between rare and common host genotypes. These results show that local adaptation results from parasite tracking of locally common host genotypes, and, as such, a necessary condition of the Red Queen hypothesis is met.

Adaptation, Physiological↗

PubMed2005

The eye of the laboratory mouse remains anatomically adapted for natural conditions.

Evolutionary effects of domestication have been demonstrated for several body systems, including the eye, and for several vertebrate species, including the mouse. Given the importance of the laboratory mouse to vision science, we wished to determine whether the anatomical and histological features of the eyes of laboratory mice are distinct from those of their naturally adapted, wild counterparts. We measured dimensions and masses of whole eyes and lenses from a wild population plus three inbred strains (C57BL/6J, NZB/BINJ, and DBA/1J) of the house house, Mus musculus, as well as wild and outbred laboratory-domesticated stock of the deer mouse, Peromyscus maniculatus. Histological preparations from these eyes were used to determine outer nuclear layer thickness, linear density of the ganglion cell layer, and for indirect immunofluorescence evaluation of cone opsin expression. For all of these traits, no statistically significant differences were found between any laboratory strain and its wild counterpart. The evolutionary effects of domestication of mice therefore do not include changes to the eye in any variable measured, supporting the continued use of this animal as a model for a naturally adapted visual system.

Animals↗

PubMed2025

Comprehensive identification and analysis of clusters of tandemly duplicated genes reveal their contributions to adaptive evolution of green plants.

Tandem gene duplication occurred more frequently compared with the episodic whole-genome duplication (WGD), providing a continuous supply of genetic material for evolutionary innovation and adaptation to changing environments. The rising roles of clusters of tandemly duplicated genes (CTDGs) in the evolution of phenotypic diversity have been unraveled in mammals. However, the content and biological roles of CTDGs remain largely unknown in plants. Here, we comprehensively identified CTDGs in 220 published plant genomes representing major lineages of green plants. The number of CTDGs showed great variation across taxa, ranging from 0 to 6028. The size of CTDGs varied from 2 to 47 genes, with small clusters containing two members predominating. Interestingly, significant expansion of CTDGs was found in early-diverging land plants and is closely associated with the evolution of key traits (e.g., ABA response, plant cuticle, UV-B resistance) required for plants to conquer terrestrial environments. Functional enrichment analysis revealed conserved and specialized functional profiles among different sizes of CTDGs in both Arabidopsis thaliana and the bryophyte Physcomitrium patens. Small CTDGs were enriched in fundamental stress responses, including protein modification, signal transduction, and responses to diverse stress stimuli, while large CTDGs were enriched in more sophisticated processes such as plant hormone biosynthesis and signaling, plant-microbe interactions, and reproductive processes. Expression pattern analyses of CTDGs under different stress conditions in A. thaliana and P. patens revealed that the highest number of CTDGs showed differential expression under drought stress, suggesting important roles of CTDGs in the evolution of desiccation tolerance in early land plants. The results of this study provide new additions to our knowledge about the abundance of CTDGs across green plants and reveal their important contributions to enable plants to overcome stressful environments on land.

Gene Duplication↗

PubMed2006

Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes.

Abstract We tested the hypothesis that phenotypic parallelism between dwarf and normal whitefish ecotypes (Coregonus clupeaformis, Salmonidae) is accompanied by parallelism in gene transcription. The most striking phenotypic differences between these forms implied energetic metabolism and swimming activity. Therefore, we predicted that genes showing parallel expression should mainly belong to functional groups associated with these phenotypes. Transcriptome profiles were obtained from white muscle by using a 3557 cDNA gene microarray developed for the Atlantic salmon (Salmo salar). A total of 1181 genes expressed in both lake populations hybridized on the array. Significant differential expression between ecotypes was detected for 134 (11.3%) and 195 (16.5%) gene clones in Cliff Lake and Indian Pond, respectively. Fifty-one genes (4.3%) showed parallel differential expression between lakes, among which 35 were expressed in opposite directions. Sixteen genes (1.35%) showed true parallelism of transcription, which mainly belonged to energetic metabolism and regulation of muscle contraction functional groups. Variance in expression was significantly reduced for these genes compared to those not showing directionality in parallelism of expression. Candidate genes associated with parallelism in swimming activity and energetic metabolism based on their level and variance in expression were identified. These results add to the growing evidence that parallel phenotypic evolution also involves parallelism at both the genotypic and regulatory level, which may at least partly be associated with genetic constraints. It also provides further evidence for the determinant role of divergent natural selection in driving phenotypic divergence, and perhaps reproductive isolation, in the adaptive radiation of lake whitefish. This study adds to a nascent field employing microarrays as powerful tools for investigating the evolutionary processes of adaptive divergence among natural populations.

Animals↗

PubMed2006

Core set approach to reduce uncertainty of gene trees.

BACKGROUND: A genealogy based on gene sequences within a species plays an essential role in the estimation of the character, structure, and evolutionary history of that species. Because intraspecific sequences are more closely related than interspecific ones, detailed information on the evolutionary process may be available by determining all the node sequences of trees and provide insight into functional constraints and adaptations. However, strong evolutionary correlations on a few lineages make this determination difficult as a whole, and the maximum parsimony (MP) method frequently allows a number of topologies with a same total branching length. RESULTS: Kitazoe et al. developed multidimensional vector-space representation of phylogeny. It converts additivity of evolutionary distances to orthogonality among the vectors expressing branches, and provides a unified index to measure deviations from the orthogoality. In this paper, this index is used to detect and exclude sequences with large deviations from orthogonality, and then selects a maximum subset ("core set") of sequences for which MP generates a single solution. Once the core set tree is formed whose all the node sequences are given, the excluded sequences are found to have basically two phylogenetic positions on this tree, respectively. Fortunately, since multiple substitutions are rare in intra-species sequences, the variance of nucleotide transitions is confined to a small range. By applying the core set approach to 38 partial env sequences of HIV-1 in a single patient and also 198 mitochondrial COI and COII DNA sequences of Anopheles dirus, we demonstrate how consistently this approach constructs the tree. CONCLUSION: In the HIV dataset, we confirmed that the obtained core set tree is the unique maximum set for which MP proposes a single tree. In the mosquito data set, the fluctuation of nucleotide transitions caused by the sequences excluded from the core set was very small. We reproduced this core-set tree by simulation based on random process, and applied our approach to many sets of the obtained endpoint sequences. Consequently, the ninety percent of the endpoint sequences was identified as the core sets and the obtained node sequences were perfectly identical to the true ones.

Animals↗

PubMed1997

Evolutionary changes of nonlinear reaction norms according to thermal adaptation: a comparison of two Drosophila species.

While the adaptive significance of discontinuous reaction norms is generally accepted, the evolutionary interpretation of continuous response curves remains speculative, and the occurrence of internal constraints is often suggested as an explanation of experimental observations. In Drosophila melanogaster, various morphometrical traits exhibit convex reaction norms to growth temperature, with a maximum value within the developmental thermal range. We compared a cold-adapted species (D. subobscura) with a mid thermal range at 16 degrees C, to the warm-adapted D. melanogaster (mid thermal range at 22 degrees C) for three different morphometrical traits: wing and thorax length in both sexes and ovariole number in females. Maximum value temperatures were ordered in the same way for the three traits in both species: ovariole number > thorax length > wing length. Significant differences were also observed between the two species for the curvature parameter of the quadratic adjustment. The major observation was a significant lateral shift in the reaction norms: maximum values were observed at much lower temperatures in the cold-adapted species than in the warm-adapted one. The parallelism between mid thermal range variation and the position of the maximum value strongly suggests an adaptive displacement of the response curves. Natural selection may thus act not only on trait mean values but also on phenotypic plasticity and on the shape of reaction norms.

Animals↗

PubMed2002

Cognitive requirements for hawk-dove games: A functional analysis for evolutionary design.

Like other social animals, humans play adaptively important games, and current evolutionary theory predicts special-purpose, domain-specific cognitive mechanisms for playing such games. We offer a functional analysis of the information requirements for successfully playing one important social game, the "hawk-dove" conflict-of-interest game, developing new graphic conventions for doing so. In particular, we address the orders of recognition necessary for successfully playing such games, showing that there are adaptive advantages of capacities for first, second, third, and fourth such orders, but no more. We suggest that first-order recognition is not only the most basic in analytic terms but is likely to have been the first to evolve, with subsequent orders added later in evolution.

Journal Article↗

PubMed2004

On the evolutionary significance of encephalization in some eutherian mammals: effects of adaptive radiation, domestication, and feralization.

Allometries of the brain to body size relationship in eutherian mammals are examined in this study as they can be used for comparative analyses concerning encephalization. In contrast with some modern presentations of this issue, an older concept is revived and expanded through this author's current study. Three allometries with clearly different slopes are valid and lead to reliable results: interspecific, intraspecific, and ontogenetic allometries. Interspecific allometries follow lines with slope values of 0.56 or 0.63 for larger and smaller species, respectively, and characterize different average encephalization plateaus with rodents and lagomorphs generally more strongly encephalized compared to basal insectivores. Artiodactyls, perissodactyls and carnivores as a whole are again on a higher but rather similar plateau. Several species of carnivores have reached different encephalization levels with respect to their average plateau indicating diverse radiations. A phylogenetic brain size increase from fossil to recent radiations is also evident. Intraspecific allometries have slope values of about 0.25. These are of help in comparing brain sizes of ancestral species with their domesticated relatives. Domestication has generally led to a brain size decrease, but species on higher encephalization plateaus show this trend more strongly than species on a lower level of encephalization. Several brain parts and the sense organs also decrease in size during the domestication process, but vary arbitrarily and to different degrees. Ontogenetic growth allometries are species-specific, but are especially different between altricial and precocial mammals. A very steep 1st phase slope of highly encephalized species is particularly useful for understanding evolutionary and adaptive phenomena. Domesticated mammals that have become feral do not show an increase in brain size despite living many generations in wild habitats.

Adaptation, Physiological↗

PubMed2000

Mental traits as fitness indicators. Expanding evolutionary psychology's adaptationism.

According to most evolutionary psychologists, human psychological adaptations can be recognized by criteria such as high efficiency, high complexity, high modularity, low phenotypic variance, low genotypic variance, low heritability, universality across cultures, and universality across individuals. These criteria are appropriate for adaptations that have been shaped through stabilizing selection for survival utility. However, they are often inappropriate for adaptations that have been shaped by sexual selection through mate choice as reliable signals of heritable fitness. If some psychological adaptations evolved as sexually selected fitness indicators of this type, we should expect them to violate many standard criteria used by evolutionary psychology to distinguish adaptations from non-adaptations. This paper addresses the problems raised by new developments in sexual selection theory and animal signaling theory for evolutionary psychology's adaptationism. It suggests that our adaptationist criteria must recognize two typical kinds of psychological adaptations: naturally selected survival mechanisms and sexually selected fitness indicators.

Adaptation, Psychological↗

PubMed2004

Bifurcation into functional niches in adaptation.

One of the central questions in evolutionary biology concerns the dynamics of adaptation and diversification. This issue can be addressed experimentally if replicate populations adapting to identical environments can be investigated in detail. We have studied 501 such replicas using digital organisms adapting to at least two fundamentally different functional niches (survival strategies) present in the same environment: one in which fast replication is the way to live, and another where exploitation of the environment's complexity leads to complex organisms with longer life spans and smaller replication rates. While these two modes of survival are closely analogous to those expected to emerge in so-called r and K selection scenarios respectively, the bifurcation of evolutionary histories according to these functional niches occurs in identical environments, under identical selective pressures. We find that the branching occurs early, and leads to drastic phenotypic differences (in fitness, sequence length, and gestation time) that are permanent and irreversible. This study confirms an earlier experimental effort using microorganisms, in that diversification can be understood at least in part in terms of bifurcations on saddle points leading to peak shifts, as in the picture drawn by Sewall Wright.

Adaptation, Biological↗

PubMed1988

Temperature adaptation of lactate dehydrogenase. Structural, functional and genetic aspects.

Comparison of the primary structures of thermophilic, mesophilic and psychrophilic lactate dehydrogenase (LDH) reveals a multitude of temperature-related amino acid substitutions. In the substitutions amino acid residues occurring preferentially in thermophilic, mesophilic (psychrophilic) LDH were found. On this basis, amino acid residues could be classified in an order from typical thermophilic (thermostabilizing) to typical mesophilic (thermolabilizing, increasing dynamics of the enzyme molecule) residues. The temperature-dependent ratio between thermostabilizing and thermolabilizing amino acid residues forms the basis for the specific structural and functional properties of thermophilic or mesophilic LDH. It is interesting that there appears to be a relationship between this order from thermophilic to mesophilic amino acid residues and the type of bases coding for these individual residues in the translation step of protein biosynthesis. Temperature-related amino acid substitutions are based on temperature-related base substitutions. A possible mechanism of temperature adaptation of LDH through alternative selection of thermophilic and mesophilic amino acid residues at the level of tRNA (anticodon)-mRNA (codon) interactions is discussed. These temperature-adaptation processes are evolutionary events in which the evolution and structure of the genetic code are involved.

Adaptation, Physiological↗

PubMed1996

Neo-Darwinian developmental evolution: can we bridge the gap between pattern and process?

In the past decade, there has been a surge of renewed interest in the study of developmental evolution. One approach that has been taken is to examine the expression patterns of a candidate gene in divergent taxa and to use these results to infer which aspects of a particular genetic pathway are either conserved or altered. Here we consider this approach from the perspective of the neo-Darwinian paradigm for evolutionary change. If adaptations are typically composed of large numbers of gene substitutions that are of small effect individually, then the candidate gene approach is unlikely to bridge the gap between developmental pattern and evolutionary process: changes in gene expression patterns may identify the steps in developmental pathways that have been altered during evolution but fail to identify the actual genetic changes that have occurred. On the other hand, there is growing support for the view that adaptations often involve large-effect genes; fortunately, the candidate gene approach is well suited to this type of genetic architecture.

Animals↗

PubMed1998

Adaptations to subordinate status in female marmoset monkeys.

In singular cooperatively breeding mammals, social status is a key determinant of female reproductive success. Usually only one dominant female breeds in a social group. In the common marmoset (Callithrix jacchus), a cooperatively breeding primate, adaptations to nonbreeding subordinate status appear to parallel those found in social insect societies which demonstrate similar skew to the marmoset in female reproductive success. Female marmosets exhibit rank-related polyethism in behavior, reproductive neuroendocrinology and non-reproductive physiology, and subordinates participate in alloparental care and territory defense. Olfactory, visual and behavioral cues from dominant female marmosets provide important proximate cues regulating ovarian inhibition in female subordinates. Cooperatively breeding marmosets, therefore, appear to have developed specific neural and neuroendocrine adaptations to subordinate social status analogous to those found in social insects such as the lower wasps, bees and termites. Such parallel developments probably reflect the outcome of repeated convergent evolutionary attempts at adapting to environmental conditions not readily conducive to dispersal and independent breeding.

Adaptation, Psychological↗

PubMed2026

Genome-wide identification and evolutionary analysis of the ERF-VII gene family in the tea plant (Camellia sinensis) and functional characterization of CsRAP2.2 in response to cold stress.

The ERF-VII gene family, a critical branch of the AP2/ERF superfamily, is central to plant stress adaptation. However, its evolutionary history and function in tea plant (Camellia sinensis) remain unclear. Here, we performed integrated evolutionary, genomic, and functional analyses of ERF-VII genes across 14 plant lineages and 20 tea plant cultivars. The phylogenetic analysis revealed that ERF-VII proteins originated after vascular plant divergence, coinciding with the emergence of the N-terminal MCGGA/I motif linked to the oxygen-dependent N-degron pathway. Gymnosperms retained few conserved members, whereas angiosperms exhibited lineage-specific expansion-extensive in monocots via whole-genome duplication, moderate in eudicots with functional diversification. Pan-genome analysis across 20 tea plant cultivars further revealed varietal differences in ERF-VII gene distribution. Transcriptome profiling via the Tea Plant Information Archive identified CsRAP2.2 as a cold-inducible ERF-VII member with sustained expression under low-temperature stress. Functional assays demonstrated that silencing CsRAP2.2 reduced cold tolerance, while overexpression in tea leaves and heterologous expression in Arabidopsis thaliana enhanced cold tolerance by maintaining photosystem II efficiency, reducing membrane lipid peroxidation, and improving antioxidant capacity. Weighted gene co-expression network analysis positioned CsRAP2.2 as a regulatory hub integrating cold, hormone, and oxygen-sensing pathways. These results clarify the evolutionary trajectory of ERF-VII genes and establish CsRAP2.2 as a core cold-tolerance regulator in tea plant. These findings may inform future breeding of cold-resilient tea cultivars.

Camellia sinensis↗

PubMed1994

Quantitative- and molecular-genetic effects on animal well-being: adaptive mechanisms.

Domestic farm animals play an important role in meeting some basic needs of humankind, especially food and clothing. The aspects of genetic improvement programs in livestock production pertinent to animal welfare and animal well-being are reviewed. A link is made between the evolutionary processes of adaptation and domestication and animal well-being. Animal behavior is a component of all these. Thus, the genetics of behavior may provide clues to the well-being of farm animal populations, and it will also be of relevance to public opinion issues of animal welfare. Many expressions of behavior by domestic livestock may be influenced by those processes that change gene as well as genotypic frequencies such as inbreeding, drift, and artificial selection. The environment in which the individual lives will also play a role, along with the interaction between genotype and environment. Selection for or against such behaviors as aggressiveness, docility, response to stress, and certain sexual behaviors in some livestock species has often been successful. This points to the existence of additive genetic variation for behavior, and scope for the inclusion of behavioral traits into selection programs, if these measures are shown to be related to welfare. Negative relationships between behaviors associated with well-being and traits of economic importance have been reported in most livestock species. However, estimates of genetic parameters, especially genetic correlations between objective measures of well-being and production traits, are scarce. There have been no comprehensive studies of the welfare of transgenic animals reported in the scientific literature. Increased use of biotechnology in animal agriculture, coupled with greater public scrutiny of livestock industries, may precipitate decisions concerning the interface of behavior and genetics that need to be addressed before scientists can conduct appropriate experimental evaluations.

Adaptation, Physiological↗

PubMed2026

Comparisons Between Large-Scale Genomic Variants and SNPs in Driving Population Divergence and Local Adaptation.

Genomic variations, such as indels (2-49 bp) and structural variants (SVs, ≥50 bp), are larger-scale mutations than single nucleotide polymorphisms (SNPs) and can substantially impact evolutionary processes, including speciation, adaptation, and phenotypes. Despite their functional importance, integrative population genetic analyses that jointly consider genome-wide SNPs, indels, and SVs remain under-explored. The ground tit (Pseudopodoces humilis), an endemic species to the Qinghai-Tibet Plateau (QTP), exhibits divergence across distinct glacial refugia, accompanied by habitat and morphological divergence, making it an excellent example for investigating how different types of genomic variants contribute to population divergence and local adaptation. Here, by retrieving 81 whole-genome sequence data, over 13 million SNPs, 2 million indels, and 22,101 SVs were identified. Variants were unevenly distributed across the genome, characterized by distinct hotspot regions. Indels and SVs revealed four genetic clusters consistent with previous SNP-based results, thereby validating the reliability of our variant datasets. FST and genotype-environment association (GEA) analyses independently revealed numerous candidate indels and SVs; each showed minimal overlap with previously identified SNPs, and were enriched in similar functional pathways such as signal transduction, skeletal muscle development, water transport, DNA repair, reproduction, nervous system development, and immunity. Collectively, our results demonstrated that indels and SVs could capture additional signatures besides SNPs. Furthermore, similar but distinct gene functions among different types of genomic variants collectively and complementarily drive genomic divergence across environmental gradients in such a high-elevation endemic species, underscoring its evolutionary relevance in local adaptation.

indels↗