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On the universality of human nature and the uniqueness of the individual: the role of genetics and adaptation.

The concept of a universal human nature, based on a species-typical collection of complex psychological adaptations, is defended as valid, despite the existence of substantial genetic variation that makes each human genetically and biochemically unique. These apparently contradictory facts can be reconciled by considering that (a) complex adaptations necessarily require many genes to regulate their development, and (b) sexual recombination makes it improbable that all the necessary genes for a complex adaptation would be together at once in the same individual, if genes coding for complex adaptations varied substantially between individuals. Selection, interacting with sexual recombination, tends to impose relative uniformity at the functional level in complex adaptive designs, suggesting that most heritable psychological differences are not themselves likely to be complex psychological adaptations. Instead, they are mostly evolutionary by-products, such as concomitants of parasite-driven selection for biochemical individuality. An evolutionary approach to psychological variation reconceptualizes traits as either the output of species-typical, adaptively designed development and psychological mechanisms, or as the result of genetic noise creating perturbations in these mechanisms.

Adaptation, Psychological↗

The evolutionary origins of electric signal complexity.

This study explores the evolutionary origins of waveform complexity in electric organ discharges (EODs) of weakly electric fish. I attempt to answer the basic question of what selective forces led to the transition from the simplest signal to the second simplest signal in the gymnotiform electric fishes. The simplest electric signal is a monophasic pulse and the second simplest is a biphasic pulse. I consider five adaptive hypotheses for the evolutionary transition from a monophasic to a biphasic EOD: (i) electrolocation, (ii) sexual selection, (iii) species isolation, (iv) territory defense, (v) crypsis from electroreceptive predators. Evaluating these hypotheses with data drawn largely from the literature, I find best support for predation. Predation is typically viewed as a restraining force on evolution of communication signals, but among the electric fishes, predation appears to have served as a creative catalyst. In suppressing spectral energy in the sensitivity range of predators (a spectral simplification), the EOD waveforms have become more complex in their time domain structure. Complexity in the time domain is readily discernable by the high frequency electroreceptor systems of gymnotiform and mormyrid electric fish. The addition of phases to the EOD can cloak the EOD from predators, but also provides a substrate for subsequent modification by sexual selection. But, while juveniles and females remain protected from predators, breeding males modify their EODs in ways that enhance their conspicuousness to predators.

Animals↗

General intelligence as a domain-specific adaptation.

General intelligence (g) poses a problem for evolutionary psychology's modular view of the human brain. The author advances a new evolutionary psychological theory of the evolution of general intelligence and argues that general intelligence evolved as a domain-specific adaptation for the originally limited sphere of evolutionary novelty in the ancestral environment. It has accidentally become universally important merely because we now live in an evolutionarily novel world. The available data seem to support the author's contention that intelligent people can solve problems better than less intelligent people only if the problems are evolutionarily novel, and they have no advantage in solving evolutionarily familiar problems. This perspective can also solve some empirical anomalies, such as the "central theoretical problem of human sociobiology" (D. R. Vining, 1986, p. 167) and the geographic distribution of general intelligence throughout the world.

Adaptation, Psychological↗

Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of algorithmic efficiency.

Algorithms↗

The role of UV-B radiation in aquatic and terrestrial ecosystems--an experimental and functional analysis of the evolution of UV-absorbing compounds.

We analysed and compared the functioning of UV-B screening pigments in plants from marine, fresh water and terrestrial ecosystems, along the evolutionary line of cyanobacteria, unicellular algae, primitive multicellular algae, charophycean algae, lichens, mosses and higher plants, including amphibious macrophytes. Lichens were also included in the study. We were interested in the following key aspects: (a) does the water column function effectively as an 'external UV-B filter'?; (b) do aquatic plants need less 'internal UV-B screening' than terrestrial plants?; (c) what role does UV screening play in protecting the various plant groups from UV-B damage, such as the formation of thymine dimers?; and (d) since early land 'plants' (such as the predecessors of present-day cyanobacteria, lichens and mosses) experienced higher UV-B fluxes than higher plants, which evolved later, are primitive aquatic and land organisms (cyanobacteria, algae, lichens, mosses) better adapted to present-day levels of UV-B than higher plants? Furthermore, polychromatic action spectra for the induction of UV screening pigments of aquatic organisms have been determined. This is relevant for translating 'physical' radiation measurements of solar UV-B into 'biological' and 'ecological' effects. From the action spectra, radiation amplification factors (RAFs) have been calculated. These action spectra allow us to determine any mitigating or antagonistic effects in the ecosystems and therefore qualify the damage prediction for the ecosystems under study. We summarize and discuss the main results based on three years of research of four European research groups. The central theme of the work was the investigation of the effectiveness of the various screening compounds from the different species studied in order to gain some perspective of the evolutionary adaptations from lower to higher plant forms. The induction of mycosporine-like amino acids (MAAs) was studied in the marine dinoflagellate Gyrodinium dorsum, the green algal species Prasiola stipitata and in the cyanobacterium Anabaena sp. While visible (400-700 nm) and long wavelength UV-A (315-400 nm) showed only a slight effect, MAAs were effectively induced by UV-B (280-315 nm). The growth of the lower land organisms studied, i.e. the lichens Cladina portentosa, Cladina foliacaea and Cladonia arbuscula, and the club moss Lycopodiumannotinum, was not significantly reduced when grown under elevated UV-B radiation (simulating 15% ozone depletion). The growth in length of the moss Tortula ruralis was reduced under elevated UV-B. Of the aquatic plants investigated the charophytes Chara aspera showed decreased longitudinal growth under elevated UV-B. In the 'aquatic higher plants' studied, Ceratophyllum demersum, Batrachium trichophyllum and Potamogeton alpinus, there was no such depressed growth with enhanced UV-B. In Chara aspera, neither MAAs nor flavonoids could be detected. Of the terrestrial higher plants studied, Fagopyrum esculentum, Deschampsia antarctica, Vicia faba, Calamagrostis epigejos and Carex arenaria, the growth of the first species was depressed with enhanced UV-B, in the second species length growth was decreased, but the shoot number was increased, and in the latter two species of a dune grassland there was no reduced growth with enhanced UV-B. In the dune grassland species studied outdoors, at least five different flavonoids appeared in shoot tissue. Some of the flavonoids in the monocot species, which were identified and quantified with HPLC, included orientin, luteolin, tricin and apigenin. A greenhouse study with Vicia faba showed that two flavonoids (aglycones) respond particularly to enhanced UV-B. Of these, quercetin is UV-B inducible and mainly located in epidermal cells, while kaempferol occurs constitutively. In addition to its UV-screening function, quercetin may also act as an antioxidant. Polychromatic action spectra were determined for induction of the UV-absorbing pigments in three photosynthetic organisms, representing very different taxonomic groups and different habitats. In ultraviolet photobiology, action spectra mainly serve two purposes: (1) identification of the molecular species involved in light absorption; and (2) calculation of radiation amplification factors for assessing the effect of ozone depletion. Radiation amplification factors (RAFs) were calculated from the action spectra. In a somewhat simplified way, RAF can be defined as the percent increase of radiation damage for a 1% depletion of the ozone layer. Central European summer conditions were used in the calculations, but it has been shown that RAF values are not critically dependent on latitude or season. If only the ultraviolet spectral region is considered, the RAF values obtained are 0.7 for the green alga Prasiola stipitata, 0.4 for the dinoflagellate Gyrodinium dorsum, and 1.0 for the cyanobacterium Anabaena sp. In the case of P. stipitata, however, the effect of visible light (PAR, photosynthetically active radiation, 400-700 nm) is sufficient to lower the RAF to about 0.4, while the PAR effect for G. dorsum is negligible. RAFs for some damage processes, such as for DNA damage (RAF=2.1 if protective effects or photorepair are not considered [1]), are higher than those above. Our interpretation of this is that if the ozone layer is depleted, increased damaging radiation could overrule increased synthesis of protective pigments. In addition to investigating the functional effectiveness of the different screening compounds, direct UV effects on a number of key processes were also studied in order to gain further insight into the ability of the organisms to withstand enhanced UV-B radiation. To this end, the temperature-dependent repair of cyclobutane dimers (CPD) and (6-4) photoproducts induced by enhanced UV-B was studied in Nicotiana tabacum, and the UV-B induction of CPD was studied in the lichen Cladonia arbuscula. Also, photosynthesis and motility were monitored and the response related to the potential function of the screening compounds of the specific organism.

Biological Evolution↗

[Adaptivity of social systems: the problem for scientific research].

The notion of adaptive evolution of social systems as of a real process of selection of the properties of such systems implies group selection. But strong evidences of effective group selection seem impossible, at least in vertebrates. However, understanding the origin of social systems adaptivity based on individual selection is difficult, as well, without analyzing the proximal mechanisms of the formation of such systems. I suppose that social systems change due to changes of individual features that underlie the proximal mechanisms of the system formation. These features are the characteristics of neurophysiological and hormonal regulatory mechanisms. They are strongly associated with intrinsic biochemical processes and are coded in the genome. Thus, the evolution of social systems is the evolution of their proximal mechanisms. At the same time, the specificity of neurophysiological and hormonal regulation determines not only social interactions, but also the individual behaviour of animals. The most important characteristics of life history, such as the regime of activity, foraging strategy, etc., are strongly affected by the same regulatory mechanisms. This view is useful for understanding the relations combining many features into an integrated and adaptive species-specific life form. I suppose that such forms emerged as evolutionary consequences of changes in regulatory mechanisms adaptive to specific environment. Thus, we have as substantial reasons to discuss adaptations of social systems to ecological features as to discuss ecological features adapted to particular social systems. The species-specificity of regulatory mechanisms is probably based on different kinds of evolutionary choice between the rapidity and the perfection of adaptation, between flexibility and stability, and between sensibility and resistibility. I think that this choice depends largely on the predictability of the environment. The less predictable it is, the more it increases the selective value of sensibility, flexibility, and rapidity of evolution. On the contrary, stable and predictable environment stimulates less rapid but more perfect adaptations. Such choices consolidate in the genome during evolution as specific features of neurophysiological and hormonal regulation systems. These specific features, in their turn, determine ecological, behavioural, and physiological species-specificity. From this point of view, evolutionary changes in social systems can be readily perceived as consequences of the selection of individuals, promoting optimal properties under particular conditional features of regulation systems. The boundary condition for this model is the absence of specificity of the characteristics of regulation systems to different forms of stress. This condition needs to be considered closely.

Adaptation, Physiological↗

Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel.

Understanding the architecture of biological adaptations is a major endeavor of evolutionary biology. Using Natural History collections, we study the genetic basis and evolution of white/brown winter coat color variation in the long-tailed weasel (Neogale frenata), a crucial phenological adaptation for camouflage in habitats with seasonal snow. We produced whole-genome sequencing data for museum specimens, along two winter color morph transition areas in North America, at the West and East coasts. Genome-wide association scans identified a single genomic region linked to color variation polymorphism with approximately 300 kb and 200 kb in the West and East regions, respectively, which included the pigmentation gene MC1R. We identified three MC1R alleles, two of which with deletions of nine or eight amino acids, alternatively associated with the winter brown morphs in the West and East, respectively. These deletions affect the second transmembrane domain, and in one case also the first extracellular loop, which in silico analyses predicted to impact the protein's function. Our findings show alternative intraspecific evolutionary solutions for environmental adaptation in long-tailed weasels, building on the evidence that major genes of the melanin production pathway are hotspots for recurrent and independent evolution of winter camouflage adaptation. This adaptive variation may be crucial to anchor adaptive responses facing future environmental change.

Receptor, Melanocortin, Type 1↗

What brought the adaptive immune system to vertebrates?--The jaw hypothesis and the seahorse.

A hypothesis is discussed that the adaptive immune system of vertebrates evolved in the gastrointestinal regions of primitive jawed fish (placoderms) due to increased localized injuries and infections which were inadvertently brought about by the novel jaw structures and the predatory life style. The question whether the modern jawless fish, cyclostomes, have adaptive immunity or not is briefly but critically reviewed. The discovery that the gut-associated immune tissues in mammals constitute the primary immune tissues for the local T cells and that some epithelial gamma delta T cells have a unique propensity is summarized and discussed in relation to the jaw hypothesis. Initial study of the seahorse (Hippocampus) indicates that the gut-associated immune tissues may be absent in this teleost species, suggesting an evolutionary link between the adaptive immune system and the jaw structure or eating habit.

Adaptation, Physiological↗

Supertree analyses of the roles of viviparity and habitat in the evolution of atherinomorph fishes.

Using supertree phylogenetic reconstructions, we investigate how livebearing and freshwater adaptations may have shaped evolutionary patterns in the Atherinomorpha, a large clade (approximately 1500 extant species) of ray-finned fishes. Based on maximum parsimony reconstructions, livebearing appears to have evolved at least four times independently in this group, and no reversions to the ancestral state of oviparity were evident. With respect to habitat, at least five evolutionary transitions apparently occurred from freshwater to marine environments, at least two transitions in the opposite direction, and no clear ancestral state was identifiable. All viviparous clades exhibited more extant species than their oviparous sister taxa, suggesting that transitions to viviparity may be associated with cladogenetic diversification. Transitions to freshwater were usually, but not invariably associated with increased species richness, but the trend was, overall, not significant among sister clades. Additionally, we investigated whether livebearing and freshwater adaptations are currently associated with elevated risks of extinction as implied by species' presence on the 2004 IUCN Red List. Despite being correlated with decreased brood size, livebearing has not significantly increased extinction risk in the Atherinomorpha. However, freshwater species were significantly more likely than marine species to be listed as endangered.

Animals↗

On the origin of genomic adaptation at high temperature for prokaryotic organisms.

For a long time, the central issue of evolutionary genomics was to find out the adaptive strategy of nucleic acid molecules of various microorganisms having different optimal growth temperatures (Topt). Long-standing controversies exist regarding the correlations between genomic G+C content and Topt, and this debate has not been yet settled. We address this problem by considering the fact that adaptation to growth at high temperature requires a coordinated set of evolutionary changes affecting: (i) nucleic acid thermostability and (ii) stability of codon-anticodon interactions. In the present study, we analyzed 16 prokaryotic genomes having intermediate G+C content and widely varying optimal growth temperatures. Results show that elevated growth temperature imposes selective constraints not only on nucleic acid level but also affects the stability of codon-anticodon interaction. We observed a decrease in the frequency of SSC and SSG codons with the increase in Topt to avoid the formation of side-by-side GC base pairs in the codon-anticodon interaction, thereby making it impossible for a genome to increase GC composition uniformly through the whole coding sequence. Thus, we suggest that any attempt to obtain a generalized relation between genomic GC composition and optimal growth temperature would hardly evolve any satisfactory result.

Adaptation, Physiological↗

The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.

Plant pan-genomics is entering a new phase beyond genome variation discovery, requiring a shift from cataloguing genomic diversity toward understanding how variation generates biological function and breeding value. Here, we propose that the future of plant pan-genomics will be shaped by three conceptual transitions. First, structural variation (SV), presence-absence variation (PAV), and haplotype diversity should be interpreted not merely as genomic differences, but as regulatory components that influence gene networks, chromatin organization, and complex traits. Second, the expansion from species-level pan-genomes to genus-level super pan-genomes provides an evolutionary framework for uncovering adaptive genetic modules preserved in wild relatives and overlooked during domestication. Third, integrating pan-genomes with pan-omics, three-dimensional genome analyses, and artificial intelligence will enable the transformation of genomic variation into predictive models for crop improvement. We further propose that the ultimate value of pan-genomes lies not in generating increasingly complete genome collections, but in establishing a mechanistic bridge between genome diversity, biological function, and breeding decisions. This transition will move crop improvement from empirical selection toward rational genome design, where evolutionary diversity can be systematically interpreted, predicted, and engineered.

Journal Article↗

Mitochondrial phylogeny of the Cyprichromini, a lineage of open-water cichlid fishes endemic to Lake Tanganyika, East Africa.

We present a phylogeny of the Cyprichromini, a lineage of cichlid fishes from Lake Tanganyika, showing progressive adaptation towards pelagic life style. Our study is based upon three mitochondrial gene segments, 443 bp of the control region, 402 bp of the cytochrome b gene and the entire NADH dehydrogenase subunit 2 gene (1047 bp). The topologies obtained by different tree building methods subdivide the Cyprichromini into four distinct lineages: the Paracyprichromis-, the Cyprichromis zonatus-, the Cyprichromis microlepidotus-lineage, and a lineage comprising Cyprichromis pavo and Cyprichromis leptosoma. Our study thus corroborates the distinctness of C. zonatus which was recently described formally. Concerning ecology and mating behavior, a clear evolutionary trend towards progressive adaptation to the pelagic zone emerges during the evolution of the Cyprichromini. The linearized tree analysis further shows that the four lineages have split almost contemporaneously. The mean Kimura-2-parameter distance among the four lineages emerging from the primary radiation of the Cyprichromini amounts to 7.21% and is in close agreement to that previously found for the primary radiation of the tribe Tropheini (7.01%), a lineage of rock-dwelling cichlids endemic to Lake Tanganyika. To date, the influence of lake level fluctuations as promoters of diversification has been demonstrated only for rock-dwelling cichlids. Based on the agreement in temporary patterns of diversification, we suggest that Pleistocene lake level changes have left a similar genetic imprint in a group of cichlid fishes that progressively colonized the open water during their radiation.

Africa, Eastern↗

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↗

Integrating historical and mechanistic biology enhances the study of adaptation.

Adding a causal, mechanistic dimension to the study of character evolution will increase the strength of inferences regarding the evolutionary history of characters and their adaptive consequences. This approach has the advantage of illuminating mechanism and testing evolutionary hypotheses rigorously. We consider the advantages of combining mechanistic and historical biology in the study of behavior, physiology, and development. We present six examples to illustrate the advantages: (1) preexisting biases in sound perception in frogs; (2) preexisting biases in visual cues in swordtailfishes; (3) exploitation of prey location behavior for attraction of mates in water mites; (4) heterospecific mating in asexual molly fishes; (5) developmental foundation of morphological diversification in amphibian digits; and (6) locomotor performance at low temperature and the evolution of nocturnality in geckos. In each of these examples, the dominant role of history, combined with organismal integration, makes ignoring history a risky proposition.

Adaptation, Physiological↗

The transcriptomics of ecological convergence between 2 limnetic coregonine fishes (Salmonidae).

Species living in comparable habitats often display strikingly similar patterns of specialization, suggesting that natural selection can lead to predictable evolutionary changes. Elucidating the genomic basis underlying such adaptive phenotypic changes is a major goal in evolutionary biology. Increasing evidence indicates that natural selection would first modulate gene regulation during the process of population divergence. Previously, we showed that parallel phenotypic adaptations of the dwarf whitefish (Coregonus clupeaformis) ecotype to the limnetic trophic niche involved parallel transcriptional changes at the same genes involved in muscle contraction and energetic metabolism relative to the sympatric normal ecotype. Here, we tested whether the same genes are also implicated in a limnetic specialist species, the cisco (Coregonus artedi), which is the most likely competitor of dwarf whitefish. Significant upregulation was detected in cisco at the same 6 candidate genes functionally involved in modulating swimming activity, namely 5 variants of a major protein of fast muscle and 1 putative catalytic crystallin enzyme. Moreover, 3 of 5 variants and the same putative catalytic crystallin enzyme were upregulated in cisco relative to the dwarf ecotype, indicating a greater physiological potential of the former for exploiting the limnetic trophic niche. This study provides the first empirical evidence that recent, parallel phenotypic evolution toward the use of the same ecological niche occupied by a specialist competitor involved similar adaptive changes in expression at the same genes. As such, this study provides strong support to the general hypothesis that directional selection acting on gene regulation may promote rapid phenotypic divergence and ultimately speciation.

Adaptation, Biological↗

Human-specific features of the cerebellum and ZP2-regulated synapse development.

Understanding the unique features of the human brain compared to non-human primates has long intrigued humankind. The cerebellum refines motor coordination and cognitive functions, contributing to the evolutionary development of human adaptability and dexterity. To identify shared and divergent features across primates, we conducted single-nucleus transcriptomic and chromatin accessibility profiling of the adult cerebellar cortex in humans, chimpanzees, macaques, and marmosets. We revealed human-specific transcriptomic and regulatory features, particularly those involved in synaptogenesis. Notably, we identified an enrichment of the sperm receptor zona pellucida glycoprotein 2 (ZP2) and its potential interactors, known for their roles in gamete interaction, in human granule cells. Experimental data show that ZP2 expression in human granule cells is induced by pontine mossy fibers, reducing synaptic proteins at pontocerebellar glomerular synapses, and decreasing cerebellar neuron electrophysiological activity. This unexpected co-option of ZP2 in human-specific synapse regulation provides insights into the evolutionary specialization of the human cerebellum.

Brain evolution↗

An analysis of mutative sigma-self-adaptation on linear fitness functions.

This paper investigates sigma-self-adaptation for real valued evolutionary algorithms on linear fitness functions. We identify the step-size logarithm log sigma as a key quantity to understand strategy behavior. Knowing the bias of mutation, recombination, and selection on log sigma is sufficient to explain sigma-dynamics and strategy behavior in many cases, even from previously reported results on non-linear and/or noisy fitness functions. On a linear fitness function, if intermediate multi-recombination is applied on the object parameters, the i-th best and the i-th worst individual have the same sigma-distribution. Consequently, the correlation between fitness and step-size sigma is zero. Assuming additionally that sigma-changes due to mutation and recombination are unbiased, then sigma-self-adaptation enlarges sigma if and only if mu < lambda/2, given (mu, lambda)-truncation selection. Experiments show the relevance of the given assumptions.

Adaptation, Biological↗

Factors underlying a latitudinal gradient in the S/G lignin monomer ratio in natural poplar variants.

The chemical composition of wood plays a pivotal role in the adaptability and structural integrity of trees. However, few studies have investigated the environmental factors that determine lignin composition and its biological significance in plants. Here, we examined the lignin syringyl-to-guaiacyl (S/G) ratio in members of a Populus trichocarpa population sourced from their native habitat and conducted a genome wide association study to identify genes linked to lignin formation. Our results revealed many significant associations, suggesting that lignin biosynthesis is a complex polygenic trait. Additionally, we found an increase in the S/G ratio from northern to southern geographic origin of the trees sampled, along with a corresponding metabolic and transcriptional reprogramming of xylem cell wall biosynthesis. Further molecular analysis identified a mutation in a cell wall laccase genetically associated with higher S/G ratios that predominate in trees from warmer lower latitudes. Collectively, our findings suggest that lignin heterogeneity arises from an evolutionary process enabling poplar adaptation to different climatic challenges.

Populus↗