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PubMed1998

Evolutionary and functional significance of hominoid tooth enamel.

The purpose of this investigation is to evaluate enamel thickness in extant and extinct hominoids. The material used in this study spans the evolutionary history of this group, from 20 million years ago to the present. The objectives of this investigation are to test three hypotheses: (1) the Loading Hypothesis: loading areas of the crown have thicker enamel than non-loading areas; (2) the Phyletic Hypothesis: differences in enamel thickness provide a basis for determining evolutionary relationships; and (3) the Functional Hypothesis: differences among hominoids result from adaptations to differing dietary and ecological habitats, that is from folivory to frugivory to hard object feeding and from tropical to forest to savanna habitats. Thin sections were prepared and polished to approximately 100 microm in thickness. Each section was then enlarged and digitally captured to the computer. Image processing and analysis software, SigmaImage (was used to measure the sections. Subsequent statistical analysis was conducted with SigmaStat and SPSS statistical software programs. The data provides statistical support for all hypotheses. In particular, the data support the proposal that "thick" enamel is the ancestral condition for the great apes and human clade. Therefore, Pongo would have retained its enamel thickness from the common ancestor of the great apes and Gorilla and Pan would have secondarily reduced enamel thickness to "thin." The common ancestor of the hominids, the australopithecines, would have "thick" enamel. The "hyper-thick" enamel of the australopithecines would be a derived character for this clade due to increased crushing and grinding and adaptation to savanna habitat. Homo would have secondarily reduced enamel thickness to "thick." Evolutionary biology of enamel differs markedly in hominids from that found in other hominoids and primates. Increased enamel thickness involved both increases in absolute thickness of enamel and crown size in response to increase masticatory loading.

Animals↗
PubMed2026

Evolutionary adaptation of CCD4 enzymes in Buddleja alternifolia for crocetin biosynthesis.

INTRODUCTION: Carotenoid cleavage dioxygenase 4 (CCD4) enzymes play central roles in carotenoid turnover and apocarotenoid biosynthesis in plants. Despite their importance, the evolutionary mechanisms underlying diversification of CCD4 catalytic functions remain poorly understood. This study investigated the CCD gene family in Buddleja alternifolia, with particular emphasis on the expansion and functional evolution of the CCD4 subfamily. METHODS: A genome-wide identification and comparative analysis of CCD genes were performed in B. alternifolia. Genomic organization, phylogenetic relationships, and syntenic patterns were analyzed to investigate gene family expansion. Functional characterization of 11 BaCCD4 paralogs was conducted through biochemical assays, while structural analyses were used to identify sequence features associated with differences in substrate cleavage specificity. Gene expression profiling was performed to assess patterns of tissue-specific regulation. RESULTS: Twenty-three CCD genes were identified, including 12 CCD4 paralogs, representing one of the largest CCD4 expansions reported within Lamiales. Syntenic and genomic analyses revealed that recent tandem duplication events, particularly within a CCD4-rich region on chromosome 10, were the primary drivers of this expansion. The presence of pseudogenes in the same region supported an ongoing birth-and-death evolutionary process. Functional analyses demonstrated extensive biochemical diversification among BaCCD4 enzymes despite their high sequence similarity. Several paralogs catalyzed asymmetric carotenoid cleavage leading to citraurin production, whereas two paralogs, KAG8367281 and KAG8375220, exhibited symmetric zeaxanthin cleavage activity, producing crocetin dialdehyde, the direct precursor of crocins. Notably, these crocetin-producing enzymes belonged to closely related paralogous pairs whose counterparts displayed distinct cleavage specificities, indicating rapid neofunctionalization after duplication. Structural analyses suggested that subtle sequence variations, including indels affecting loop regions adjacent to the substrate access channel, may underlie changes in regioselectivity. Expression profiling further revealed tissue-specific expression patterns consistent with functional divergence among paralogs. DISCUSSION: These findings indicate that crocetin-forming activity in B. alternifolia likely evolved through progressive modifications of ancestral CCD4 functions rather than through a single evolutionary event. The remarkable expansion and diversification of the CCD4 subfamily provide evidence for the role of gene duplication and neofunctionalization in shaping carotenoid cleavage specificity. Collectively, this work establishes B. alternifolia as a valuable model for investigating the molecular evolution of CCD4 enzymes and the emergence of specialized apocarotenoid metabolism in plants.

CCD4 evolution↗
PubMed2026

Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.

Long runtimes, high memory demands, and reliance on high-performance computing impede phylogenomic analyses. We review a scalable phylogenomic subsampling with upsampling (PSU) framework, in which small subsamples of sites from a concatenated alignment are expanded by upsampling before inference, and the resulting analyses are then aggregated to obtain evolutionary estimates. PSU harnesses the fact that the computational cost of maximum likelihood analysis is strongly influenced by the number of distinct site patterns in the concatenated alignment, whereas statistical power depends primarily on the amount of evolutionary information represented by the total number of sites and substitutions. By reducing the former while restoring the latter through upsampling, PSU can approximate many full-data analyses at substantially lower computational cost. Analysis of simulated and empirical datasets shows that PSU can accurately estimate bootstrap support values, select the optimal substitution model, test evolutionary hypotheses, and infer branch lengths, divergence times, and associated uncertainty measures, while reducing runtime and memory requirements by orders of magnitude. PSU also provides distributions of inferred clade support across independent subsamples, enabling detection of conflicting phylogenetic signals that may remain hidden in conventional bootstrap analysis. Automated tuning of subsample size, the number of subsamples, and the number of upsampling replicates make PSU practical across diverse datasets. We suggest that PSU is a general strategy for scalable phylogenomic inference using a broad range of statistical methods. By enabling analyses of genome-scale alignments on commodity hardware, PSU broadens research access and reduces environmental and infrastructural costs of big-data phylogenomics.

confidence limits↗
PubMed1997

Removing irrelevant features in neural network classification using evolutionary computations.

Evolutionary artificial neural networks (EANN) are a new paradigm that refers to a special class of artificial neural networks (ANN) in which evolution is another fundamental form of adaptation in addition to learning. Evolution can be introduced at various levels of ANN. It can be used to evolve weights, architectures and learning parameters. Evolutionary computations are population-based search methods that have shown promise in many similarly complex tasks. This paper presents an application of evolutionary programming for simultaneously inducing the input structure and weights evolving for multilayer feed-forward perceptrons (MLP) with standard sigmoidal activation function.

Algorithms↗
PubMed1999

[Evolutionary ecology and epidemiology of interactions between Anopheles mosquitoes and malaria].

The transmission of malaria is largely determined by two parameters: the biting rate of the mosquito vector and its mortality. In this paper, data on the interactions among these parameters are reviewed to describe possible evolutionary mechanisms underlying the parasite's life cycle. In particular, in contrast to conventional wisdom about medical entomology, the author suggests that malaria parasites are not always expected to minimise the damage they inflict on their mosquito host. Rather, when they have developed into the infectious stage, they can increase their transmission by manipulating the mosquito to bite more frequently; this, however, is associated with a higher risk of being killed by the human host. This example illustrates that parameters determining malaria transmission can only be understood by integrating ecological and evolutionary ideas into more traditional epidemiology. Such an evolutionary view of malaria and mosquitoes will eventually lead to a better understanding of the epidemiology of malaria and may help to predict the effect of malaria control.

Animals↗
PubMed1999

[Evolutionary biological discoveries can increase the understanding of cardiovascular diseases. It can contribute to more realistic preventive strategies].

Recent findings in evolutionary biology offer new insights into the historical emergence of widespread medical disorders such as cardiovascular disease and type 2 diabetes. This has been named evolutionary medicine. When individuals with a genetic program for retention of sodium and calories (insulin resistance) encounter the stress and unwholesome lifestyle of modern society, cardiovascular disease may soon develop, potential consequences being myocardial infarction or stroke. Focusing on historical changes in climate, social circumstances and food availability in the Nordic countries, factors which very much defined living conditions for our ancestors, we discuss cardiovascular disease from the point of view of evolutionary medicine. A better understanding of this perspective will hopefully increase the likelihood of success in preventive efforts such as lifestyle intervention.

Biological Evolution↗
PubMed2000

Evolutionary history of the uterine serpins.

A bioinformatics analysis was conducted on the four members of the uterine serpin (US) family of serpins. Evolutionary analysis of the protein sequences and 86 homologous serpins by maximum parsimony and distance methods indicated that the uterine serpins proteins form a clade distinct from other serpins. Ancestral sequences were reconstructed throughout the evolutionary tree by parsimony. These suggested that some branches suffered a high ratio of nonsynonymous to synonymous mutations, suggesting episodes of adaptive evolution within the serpin family. Analysis of the sequences by neutral evolutionary distance methods suggested that the uterine serpins diverged from other serpins prior to the divergence of the mammals from other vertebrates. The porcine uterine serpins are paralogs that diverged from a single common ancestor within the Sus genus after pigs separated from other artiodactyls. The uterine serpins contain several protein kinase C and tyrosine kinase phosphorylation sites. These sites may be important for the lymphocyte-inhibitory activity of OvUS if, like other basic proteins, OvUS can cross the cell membrane of an activated lymphocyte. Internalized OvUS could serve as an alternative target to protein kinases important for the mitogenic response to antigens.

Amino Acid Sequence↗
PubMed1999

Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements.

The availability of the complete genome sequence of Saccharomyces cerevisiae provides the unique opportunity to study an entire genomic complement of retrotransposons from an evolutionary perspective. There are five families of yeast retrotransposons, Ty1-Ty5. We have conducted a series of comparative sequence analyses within and among S. cerevisiae Ty families in an effort to document the evolutionary forces that have shaped element variation. Our results indicate that within families Ty elements vary little in terms of both size and sequence. Furthermore, intra-element 5'-3' long terminal repeat (LTR) sequence comparisons indicate that almost all Ty elements in the genome have recently transposed. For each family, solo LTR sequences generated by intra-element recombination far outnumber full length insertions. Taken together, these results suggest a rapid genomic turnover of S. cerevisiae Ty elements. The closely related Ty1 and Ty2 are the most numerous elements in the genome. Phylogenetic analysis of full length insertions reveals that reverse transcriptase mediated recombination between Ty1 and Ty2 elements has generated a number of hybrid Ty1/2 elements. These hybrid Ty1/2 elements have similar genomic structures with chimeric LTRs and chimeric TYB (pol) genes. Analysis of the levels of nonsynonymous (Ka) and synonymous (Ks) nucleotide variation indicates that Ty1 and Ty2 coding regions have been subject to strong negative (purifying) selection. Distribution of Ka and Ks on Ty1, Ty2 and Ty1/2 phylogenies reveals evidence of negative selection on both internal and external branches. This pattern of variation suggests that the majority of full length Ty1, Ty2 and Ty1/2 insertions represent active or recently active element lineages and is consistent with a high level of genomic turnover. The evolutionary dynamics of S. cerevisae Ty elements uncovered by our analyses are discussed with respect to selection among elements and the interaction between the elements and their host genome.

Amino Acid Sequence↗
PubMed2000

Evolutionary malignant resistance of cells to damaging factors as common biological defence mechanism in neoplastic development. Review of conception.

Cells have some inborn resistance to harmful factors, which could be called physiological or natural resistance. The mechanisms of multixenobiotic resistance (MXR) and multidrug resistance (MDR) have common features in the formation of acquired resistance in microorganisms, carcinogenesis, tumour metastases and chemotherapy or irradiation. ATP-dependent membrane P-glycoprotein, as an MDR efflux pump, glutathione S-transferases and other products of evolutionary resistance-related genes arised for exportation and detoxification of cytotoxic xenobiotics and drugs are transmitted from bacteria to man. On the one hand, this evolutionary MXR as a common biological defence mechanism is a "driving" power to conserve homeostasis of cells, tissues and organs. On the other hand, mutation, selection and simplification of properties are the causes of functional and morphological changes in tumour cells which regress to a more primitive mode of existence (atavism) for adaptation to survival. In the present work are presented data on the forms of E. coli resistant to antibiotics and of sarcoma 45 resistant to alkylic preparations. They may be helpful in revealing the causes of resistance and acquired accelerated growth of cells. The development of tumours as fibromas 14-15 years following injection of a vital dye trypan blue into human skin supports our conception that neoplastic growth is a particular case of the evolutionary resistance of cells adapted to the damaging factors. So, tumour cells adopting the enhancement mechanisms of general biological persistent resistance, i. e. undergoing repeated cycles of malignancy enhancement, adapt themselves to survive under the changed unfavourable conditions.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2001

Evolutionary approach to medicine.

A new discipline in the medical field, called Darwinian (or evolutionary) Medicine, has arisen to study how natural selection could shape a machine as complex as the human body without eliminating its vulnerability to diseases. It asserts that systems and organs that form our bodies result from millions of years of evolutionary advances and are designed to survive in order to reproduce. According to this principle, Nature does not strive for complexity or perfection-it is blind and random. Using the scientific knowledge that has revolutionized biology, Darwinian Medicine seeks to provide an explanation for diseases based on the evolutionary process. This new discipline, in short, can undoubtedly help physicians in their medical practice, though further research is necessary to improve understanding of the range of its clinical application.

Biological Evolution↗
PubMed2001

Homosexual orientation in males: evolutionary and ethological aspects.

Evolutionary theory proposes that adaptive traits are reproduced more successfully than maladaptive traits. Accordingly, natural selection should favor heterosexuality as it facilitates reproduction and the propagation of genes. However, the question becomes, what has maintained homosexuality in a small but consistent percentage of the human population? Research into the evolutionary and hormonal factors associated with a homosexual orientation have yielded provocative but inconsistent results. It also suggests that human sexual orientation, and in particular homosexual orientation, is too complex to be described by one simple model or a single research discipline. The current paper treads a new path and emphasizes an integrative approach for the understanding of homosexuality. The authors examine the combined effects of evolutionary factors and neurohormonal processes on the development of a homosexual orientation. It is suggested that research into the topic could benefit from an examination of and change in some of the assumptions upon which much past research has been based.

Adaptation, Physiological↗
PubMed2001

Evolutionary attempts at 4 eyes in vertebrates.

PURPOSE: To understand and compare the optical, histological, and ecological differences among 4 vertebrate species that have had evolutionary attempts toward 4 eyes. METHODS: An evolutionary attempt at 4 eyes in defined as the duplication or one or more structures integral to the refraction or interpretation of the visible spectrum for that animal. We reviewed and compared the known optics, histology, and ecology of each of these vertebrate species with attempts at 4 eyes including Anableps anableps, Dialomnus fuscus, Mnierpes macrocephalus, and Bathylychnops exilis. These animals have developed portions of ancillary eyes that have diverged from the primary globe in 3 different patterns. At least 1 specimen of each of those vertebrate species known to have 4 eyes was examined histologically and compared to the animal's ecology and current cladistic relationship. RESULTS: A anabteps has 2 distinct optical systems in each eye: an upper one for aerial vision and a lower system for aquatic vision. These systems feature separate retinae and an asymmetric lens to achieve focus in the aerial and aquatic vision, but only 1 optic nerve per eye. The visual system is split horizontally to function optimally in a "prone" position in the water. D fuscus is a terrestrial feeder and has a vertically (almost perpendicular to the long axis of the fish) divided cornea using pigment and a condensation of collagen as the divider, a single pupil, and a divided retina. The split cornea allows for the fish to remain vertical with 1 cornea in air and 1 cornea in water. M macrocephalus is probably closely related to D fuscus with a similar split cornea. B exilis is a mesopelagic inhabitant living at approximately 200 to 1,000 m and has an ancillary globe that "buds" off the primary globe. This secondary globe is directed inferiorly toward the ocean floor as compared to the primary globe, which is directed 35 degrees superiorly from the horizontal. Adult species of B exilis have 2 additional scleral bodies suspected to be lenses. If so, these structures would be capable of focusing light from the inferior field onto the superior retina, presumably adding to the panoramic inferior visual field. There are other mesopelagic species, including Styleophorus chordatus, Opisthoproctus grimaldii, Scopelarchus gantheri (or guentheri), Dolichopteryx binocularis, Benthalbella infans, and Evermannella indica, that have other unusual ocular mechanisms, such as retinal diverticulae and lens pads capable of reflection, but do not meet the definition of multiple eyes, as defined for purposes of this work. CONCLUSIONS: D fuscus and M macrocephalus are terrestrial feeders requiring aquatic and aerial vision, and hence have a split cornea for this purpose, and they probably use their anterior corneae for terrestrial vision. A anableps swims at the surface with combined aerial and aquatic vision for feeding and protection from predators. B exilis is a mesopelagic feeder requiring a binocular visual field in the horizontal meridian and above, and simultaneously is a bottom scavenger using an ancillary globe and perhaps scleral lenses for recognition of bioluminescent detritus. Although 2 of these models are related (D fuscus and M macrocephalus), these 4 fish represent 3 separate, distinct, and unrelated convergent evolutionary attempts toward 4 eyes in vertebrates satisfying the ecological needs of each. The 3 different models are unrelated evolutionarily and are found in 3 separate orders.

Animals↗
PubMed2001

Rates of evolution on the time scale of the evolutionary process.

A generational time scale, involving change from one generation to the next, is the time scale of evolution by natural selection. Microevolutionary and macroevolutionary patterns reflect this process on longer time scales. Rates of evolution are most efficiently expressed in haldane units, H, in standard deviations per generation, indexed by the log of the time interval. Rates from replicated selection experiments and simulations have rate-interval [RI] and log rate-log interval [LRI] scaling relations enabling directional, stationary, and random time series to be distinguished. Empirical microevolutionary and macroevolutionary data exhibit stationary scaling, but point to generational rates of evolution (H0) conservatively on the order of 0.2 standard deviations per generation on the time scale of the evolutionary process. This paradox of long-term stationary scaling and short-term high rates of change can be explained by considering the shape of an heuristic time-form evolutionary lattice. Cenozoic mammals occupy a lattice that is about four orders of magnitude longer in time than it has ever been wide in form. The evolutionary process is dynamic but operates within relatively narrow morphological constraints compared to the time available for change.

Animals↗
PubMed2001

Population structure inhibits evolutionary diversification under competition for resources.

A model is presented that explores how population structure affects the evolutionary outcome of ecological competition for resources. The model assumes that competition for resources occurs within groups of a finite number of individuals (interaction groups), and that limited dispersal of individuals between groups (according to Wright's island model of population structure) results in genetic structuring of the population. It is found that both finite-sized interaction groups and limited dispersal can have substantial effects on the evolution of resource exploitation strategies as compared to models with a single, infinitely large, well-mixed interaction group. Both effects, in general, tend to select for less aggressive competitive strategies. Moreover, both effects also tend to reduce the likelihood of the evolutionary diversification of resource exploitation strategies that often occurs in models of resource competition with infinite populations. The results are discussed in the context of theories of the evolutionary diversification of resource exploitation strategies and speciation.

Biological Evolution↗
PubMed2002

Using evolutionary methods to study G-protein coupled receptors.

A novel method to analyze evolutionary change is presented and its application to the analysis of sequence data is discussed. The investigated method uses phylogenetic trees of related proteins with an evolutionary model in order to gain insight about protein structure and function. The evolutionary model, based on amino acid substitutions, contains adjustable parameters related to amino acid and sequence properties. A maximum likelihood approach is used with a phylogenetic tree to optimize these parameters. The model is applied to a set of Muscarinic receptors, members of the G-protein coupled receptor family. Here we show that the optimized parameters of the model are able to highlight the general structural features of these receptors.

Animals↗
PubMed2002

Darwinian medicine: applications of evolutionary biology for veterinarians.

Every medical phenomenon has both a mechanistic explanation and an evolutionary explanation. Veterinarians are accustomed to dealing with the mechanistic, the "what" or the "how", of various disease conditions, and applying treatment accordingly. Darwinian medicine is a field that addresses the evolutionary explanation, the "why" for various medical conditions. This review focuses on these Darwinian explanations and is divided into 4 main categories--host defenses, virulence, genetic conflict, and incomplete adaptation to a changing environment. Each of these areas is reviewed, with examples of evolutionary reasons for disease conditions. Consideration of adaptationist reasons for many of these disease phenomena should make veterinarians better clinicians, educators, and researchers.

Adaptation, Biological↗
PubMed2002

[Variation of loci encoding homologous enzymes in an evolutionary series of vertebrates].

A study of variability of 11 allozyme loci (sAat, G3pdh, Gpi, sIdh, Ldh-A, Ldh-B, sMdh, sMe, sSod, Pgdh, and Sdh) in the evolutionary series of vertebrates from Cyclostomat to Mammalia revealed that (1) in vertebrates, these loci encoding multimeric enzymes are characterized by different heterozygosity levels, the extremes of which (represented by loci Ldh-A and Pgdh) differ from each other more than by a factor of 4; (2) classes of vertebrates markedly differed from one another in genetic variation; lower Tetrapoda are characterized by the highest level of genetic polymorphism, the classes representing the margins of the phyletic line-primitive (Cyclostomata and Chondrchthyes) and advanced (Aves and Mammalia)--have minimum heterozygosity levels, whereas Osteichthyes are characterized by intermediate heterozygosity level; (3) in the evolutionary series of vertebrates, heterozygosity varies rather independently in the groups of loci characterized by low, medium, and high variability. These patterns are explained in the context of intraorganismic factors: integration of mono- and polygenic traits (primarily, body size and ontogeny rate) and evolutionary specialization.

Animals↗
PubMed2002

Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind.

Evolutionary psychologists often overlook a wealth of information existing between the proximate genotypic level and the ultimate phenotypic level. This commonly ignored level of biological organization is the ongoing activity of neurobiological systems. In this paper, we extend our previous arguments concerning strategic weaknesses of evolutionary psychology by advocating a foundational view that focuses on similarities in brain, behavior, and various basic psychological features across mammalian species. Such an approach offers the potential to link the emerging discipline of evolutionary psychology to its parent scientific disciplines such as biochemistry, physiology, molecular genetics, developmental biology and the neuroscientific analysis of animal behavior. We detail an example of this through our impending work using gene microarray technology to characterize gene expression patterns in rats during aggressive and playful social interactions. Through a focus on functional homologies and the experimental analysis of conserved, subcortical emotional and motivational brain systems, neuroevolutionary psychobiology can reveal ancient features of the human mind that are still shared with other animals. Claims regarding evolved, uniquely human, psychological constructs should be constrained by the rigorous evidentiary standards that are routine in other sciences.

Adaptation, Psychological↗