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PubMed1991

Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes.

Although it is widely accepted that the plastids of plants and algae originated as endosymbionts, the details of this evolutionary process are unclear. It has been proposed that in organisms whose plastids are surrounded by more than two membranes, the endosymbiont was a eukaryotic alga rather than a photosynthetic prokaryote. The DNA-containing nucleomorph of cryptomonad algae appears to be the vestigial nucleus of such an algal endosymbiont. Eukaryotic-type ribosomal RNA sequences have been localized to a nucleolus-like structure in the nucleomorph. In support of the hypothesis that cryptomonads are evolutionary chimaeras of two distinct eukaryotic cells, we show here that Cryptomonas phi contains two phylogenetically separate, nuclear-type small-subunit rRNA genes, both of which are transcriptionally active. We incorporate our rRNA sequence data into phylogenetic trees, from which we infer the evolutionary ancestry of the host and symbiont components of Cryptomonas phi. Such trees do not support the thesis that chromophyte algae evolved directly from a cryptomonad-like ancestor.

Animals↗

PubMed1993

Confidence in evolutionary trees from biological sequence data.

The reliable construction of evolutionary trees from nucleotide sequences often depends on randomization tests such as the bootstrap and PTP (cladistic permutation tail probability) tests. The genomes of bacteria, viruses, animals and plants, however, vary widely in their nucleotide frequencies. Where genomes have independently acquired similar G+C base compositions, signals in the data arise that cause methods of evolutionary tree reconstruction to estimate the wrong tree by grouping together sequences with similar G+C content. Under these conditions randomization tests can lead to both the rejection of the correct evolutionary hypothesis and acceptance of an incorrect hypothesis (such as with the contradictory inferences from the photosynthetic rbcS and rbcL sequences). We have proposed one approach to testing for G+C content problem. Here we present a formalization of this method, a frequency-dependent significance test, which has general application.

Base Sequence↗

PubMed2002

The emerging conceptual framework of evolutionary developmental biology.

Over the last twenty years, there has been rapid growth of a new approach to understanding the evolution of organismic form. This evolutionary developmental biology, or 'evo-devo', is focused on the developmental genetic machinery that lies behind embryological phenotypes, which were all that could be studied in the past. Are there any general concepts emerging from this new approach, and if so, how do they impact on the conceptual structure of traditional evolutionary biology? In providing answers to these questions, this review assesses whether evo-devo is merely filling in some missing details, or whether it will cause a large-scale change in our thinking about the evolutionary process.

Anatomy, Comparative↗

PubMed2002

Computational and evolutionary aspects of language.

Language is our legacy. It is the main evolutionary contribution of humans, and perhaps the most interesting trait that has emerged in the past 500 million years. Understanding how darwinian evolution gives rise to human language requires the integration of formal language theory, learning theory and evolutionary dynamics. Formal language theory provides a mathematical description of language and grammar. Learning theory formalizes the task of language acquisition it can be shown that no procedure can learn an unrestricted set of languages. Universal grammar specifies the restricted set of languages learnable by the human brain. Evolutionary dynamics can be formulated to describe the cultural evolution of language and the biological evolution of universal grammar.

Biological Evolution↗

PubMed2004

Emergence of cooperation and evolutionary stability in finite populations.

To explain the evolution of cooperation by natural selection has been a major goal of biologists since Darwin. Cooperators help others at a cost to themselves, while defectors receive the benefits of altruism without providing any help in return. The standard game dynamical formulation is the 'Prisoner's Dilemma', in which two players have a choice between cooperation and defection. In the repeated game, cooperators using direct reciprocity cannot be exploited by defectors, but it is unclear how such cooperators can arise in the first place. In general, defectors are stable against invasion by cooperators. This understanding is based on traditional concepts of evolutionary stability and dynamics in infinite populations. Here we study evolutionary game dynamics in finite populations. We show that a single cooperator using a strategy like 'tit-for-tat' can invade a population of defectors with a probability that corresponds to a net selective advantage. We specify the conditions required for natural selection to favour the emergence of cooperation and define evolutionary stability in finite populations.

Biological Evolution↗

PubMed2005

Evolutionary dynamics on graphs.

Evolutionary dynamics have been traditionally studied in the context of homogeneous or spatially extended populations. Here we generalize population structure by arranging individuals on a graph. Each vertex represents an individual. The weighted edges denote reproductive rates which govern how often individuals place offspring into adjacent vertices. The homogeneous population, described by the Moran process, is the special case of a fully connected graph with evenly weighted edges. Spatial structures are described by graphs where vertices are connected with their nearest neighbours. We also explore evolution on random and scale-free networks. We determine the fixation probability of mutants, and characterize those graphs for which fixation behaviour is identical to that of a homogeneous population. Furthermore, some graphs act as suppressors and others as amplifiers of selection. It is even possible to find graphs that guarantee the fixation of any advantageous mutant. We also study frequency-dependent selection and show that the outcome of evolutionary games can depend entirely on the structure of the underlying graph. Evolutionary graph theory has many fascinating applications ranging from ecology to multi-cellular organization and economics.

Biological Evolution↗

PubMed2026

Comparative mitogenomics of Ocnus glacialis reveals lineage-specific evolutionary rates and complex gene rearrangements in Dendrochirotida.

The order Dendrochirotida (Class Holothuroidea) is a species-rich echinoderm group, yet its internal evolutionary history remains poorly resolved due to limited mitogenomic resources. In this study, we characterized the first complete mitochondrial genome of Ocnus glacialis and conducted comparative analyses to elucidate its phylogenetic position and molecular evolutionary patterns. The circular mitogenome of O. glacialis is 16,776 bp in length, containing the canonical set of 37 genes. Among the analyzed dendrochirotids, O. glacialis exhibited the highest A + T content (70.88%) and a near-zero AT-skew, a compositional profile often linked to lineage-specific evolution in specialized environments. Selection pressure analyses, including branch-model tests, revealed that these compositional features are associated with relaxed purifying selection and an accelerated rate of sequence evolution. Branch-site analyses further identified specific codon sites in cytb, nad2, nad4l, nad5, and nad6 under positive or relaxed constraints. Structurally, O. glacialis displayed the most complex gene rearrangement pattern among the studied species, characterized by multiple tandem duplication-random loss (TDRL) events and extensive intergenic sequences. Furthermore, divergence time estimation suggests that these structural and compositional shifts occurred in tandem with the lineage's diversification. We propose that these mitogenomic signatures reflect a synergistic outcome of habitat transition toward Arctic cold-water and deep-sea environments, coupled with demographic factors such as reduced effective population sizes inherent to its benthic life history. By resolving taxonomic uncertainties, this study provides a robust temporal and molecular framework for understanding the evolutionary history and ecological diversification of the Ocnus lineage.

Animals↗

PubMed2006

The conversion of variance and the evolutionary potential of restricted recombination.

Genetic recombination is usually considered to facilitate adaptive evolution. However, recombination prevents the reliable cotransmission of interacting gene combinations and can disrupt complexes of coadapted genes. If interactions between genes have important fitness effects, restricted recombination may lead to evolutionary responses that are different from those predicted from a purely additive model and could even aid adaptation. Theory and data have demonstrated that phenomena that limit the effectiveness of recombination via increasing homozygosity, such as inbreeding and population subdivision and bottlenecks, can temporarily increase the additive genetic variance available to these populations. This effect has been attributed to the conversion of nonadditive to additive genetic variance. Analogously, phenomena such as chromosomal inversions and apomictic parthenogenesis that physically restrict recombination in part or all of the genome may also result in a release of additive variance. Here, we review and synthesize literature concerning the evolutionary potential of populations with effectively or physically restricted recombination. Our goal is to emphasize the common theme of increased short-term access to additive genetic variance in all of these situations and to motivate research directed towards a more complete characterization of the relevance of the conversion of variance to the evolutionary process.

Animals↗

PubMed2006

Quantitative and evolutionary biology of alternative splicing: how changing the mix of alternative transcripts affects phenotypic plasticity and reaction norms.

Alternative splicing (AS) of pre-messenger RNA is a common phenomenon that creates different transcripts from a single gene, and these alternative transcripts affect phenotypes. The majority of AS research has examined tissue and developmental specificity of expression of particular AS transcripts, how this specificity affects cell function, and how aberrant AS is related to disease. Few studies have examined quantitative between-individual variation in AS within a cell or tissue type, or in relation to phenotypes, but the results are compelling: quantitative variation in AS affects plastic traits such as stress, anxiety, fear, egg production, muscle performance, energetics and plant growth. Genomic analyses of AS are also at a nascent stage, but have revealed a number of significant evolutionary patterns. Growing knowledge of upstream genes and kinases that regulate AS provides the as-yet little explored potential to examine how these genes and pathways respond to environmental and genotype variables. Research in this area can provide glimpses of a labyrinth of genetic architectures that have rarely been considered in evolutionary and organismal biology, or in quantitative genetics. The scarcity of contribution to knowledge about AS from these fields is illustrated by the fact that heritability of quantitative variation in AS has not yet been determined for any gene in any organism. New research tactics that incorporate quantitative analyses of AS will allow organismal and evolutionary biologists to attain a fuller mechanistic understanding of many of the traits they study, and may lead to more rapid discovery of functionally important polymorphisms.

Alternative Splicing↗

PubMed2000

Is there an evolutionary mismatch between the normal physiology of the human dopaminergic system and current environmental conditions in industrialized countries?

A large body of evidence has recently defined a field theory known as 'evolutionary mismatch', which derives its attributes largely from the fact that current environmental conditions are completely different from those in which the human central nervous system evolved. Current views on the evolutionary mismatch theory lack, however, any attempts to define which brain areas or neuronal circuits should be mostly involved in coding such misevolved traits and to what extent our neurobiological knowledge can be applied to the topographical localization of a specific psychopathology. In this respect the mesocorticolimbic dopaminergic circuits have long been misconceptualized as simple reward or reinforcement systems. Instead, they motivate and coordinate the functions of the higher brain areas that mediate planning and foresight and direct finalized movement in both animals and humans. These systems make animals intensely interested in exploring the world around them, but by the same means they also make them susceptible to the environmental stimuli that have been sought and consumed. It is has been speculated that the cortical dopamine targets that developed most recently in phylogeny are of particular functional value, and that the mesocorticolimbic dopaminergic system is involved in more complex integrative functions than previously assumed. In the present paper I will argue that some mental disorders may have their deep roots in the evolutionary mismatch between the normal physiology of the mesocorticolimbic dopaminergic system and the current environmental conditions in affluent societies.

Animals↗

PubMed1999

Evolutionary conservation and somatic mutation hotspot maps of p53: correlation with p53 protein structural and functional features.

Missense mutations in p53 frequently occur at 'hotspot' amino acids which are highly conserved and represent regions of structural or functional importance. Using the p53 mutation database and the p53 DNA sequences for 11 species, we more precisely defined the relationships among conservation, mutation frequency and protein structure. We aligned the p53 sequences codon-by-codon and determined the degree of substitution among them. As a whole, p53 is evolving at an average rate for a mammalian protein-coding gene. As expected, the DNA binding domain is evolving more slowly than the carboxy and amino termini. A detailed map of evolutionary conservation shows that within the DNA binding domain there are repeating peaks and valleys of higher and lower evolutionary constraint. Mutation hotspots were identified by comparing the observed distribution of mutations to the pattern expected from a random multinomial distribution. Seventy-three hotspots were identified; these 19% of codons account for 88% of all reported p53 mutations. Both high evolutionary constraint and mutation hotspots are noted at amino acids close to the protein-DNA interface and at others more distant from DNA, often buried within the core of the folded protein but sometimes on its surface. The results indicate that targeting highly conserved regions for mutational and functional analysis may be efficient strategies for the study of cancer-related genes.

Chromosome Mapping↗

PubMed2002

Psychotropic substance-seeking: evolutionary pathology or adaptation?

According to a conventional evolutionary perspective, the human propensity for substance use is the product of a 'mismatch' between emotional mechanisms that evolved in a past without pure drugs or direct routes of drug administration, and the occurrence of these phenomena in the contemporary environment. The primary purpose of this review is to assert that, contrary to the conventional view, humans have shared a coevolutionary relationship with psychotropic plant substances that is millions of years old. We argue that this 'deep time' relationship is self-evident both in the extant chemical-ecological adaptations that have evolved in mammals to metabolize psychotropic plant substances and in the structure of plant defensive chemicals that have evolved to mimic the structure, and interfere with the function, of mammalian neurotransmitters. Given this evidence, we question how emotional mechanisms easily triggered by plant toxins can have evolved. Our argument is also supported with archeological and historical evidence of substance use in antiquity suggesting that, for people in the past, psychotropic plant substances were as much a mundane everyday item as they are for many people today. Our second, and more speculative objective is to suggest provisional hypotheses of human substance-using phenomena that can incorporate the evolutionary implications of a deep time relationship between psychotropic substances and people. We discuss hypotheses of selective benefits of substance use, including the idea that neurotransmitter-analog plant chemicals were exploited as substitutes for costly, nutritionally constrained endogenous neurotransmitters. However, even if substance seeking was adaptive in the environment of our hominid ancestors, it may not still be so in the contemporary environment. Thus, the implications of our argument are not that the mismatch concept does not apply to human substance-using phenomena, but that it must be reconsidered and extended to incorporate the implications of a substance-rich, rather than substance-free, evolutionary past.

Adaptation, Physiological↗

PubMed1998

Comparative mtDNA phylogeography of neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America.

Historical biogeography seeks to explain contemporary distributions of taxa in the context of intrinsic biological and extrinsic geological and climatic factors. To decipher the relative importance of biological characteristics vs. environmental conditions, it is necessary to ask whether groups of taxa with similar distributions share the same history of diversification. Because all of the taxa will have shared the same climatic and geological history, evidence of shared history across multiple species provides an estimate of the role of extrinsic factors in shaping contemporary biogeographic patterns. Similarly, differences in the records of evolutionary history across species will probably be signatures of biological differences. In this study, we focus on inferring the evolutionary history for geographical populations and closely related species representing three genera of primary freshwater fishes that are widely distributed in lower Central America (LCA) and northwestern Colombia. Analysis of mitochondrial gene trees provides the opportunity for robust tests of shared history across taxa. Moreover, because mtDNA permits inference of the temporal scale of diversification we can test hypotheses regarding the chronological development of the Isthmian corridor linking North and South America. We have focused attention on two issues. First, we show that many of the distinct populations of LCA fishes diverged in a relatively brief period of time thus limiting the phylogenetic signal available for tests of shared history. Second, our results provide reduced evidence of shared history when all drainages are included in the analysis because of inferred dispersion events that obscure the evolutionary history among drainage basins. When we restrict the analysis to areas that harbour endemic mitochondrial lineages, there is evidence of shared history across taxa. We hypothesize that there were two to three distinct waves of invasion into LCA from putative source populations in northwestern Colombia. The first probably happened in the late Miocene, prior to the final emergence of the Isthmus in the mid-Pliocene; the second was probably coincident with the rise of the Isthmus in the mid-Pliocene, and the third event occurred more recently, perhaps in the Pleistocene. In each case the geographical scale of the dispersion of lineages was progressively more limited, a pattern we attribute to the continuing development of the landscape due to orogeny and the consequent increase in the insularization of drainage basins. Thus, the fisheye view of LCA suggests a complex biogeographic history of overlaid cycles of colonization, diversification, sorting and extinction of lineages.

ATP Synthetase Complexes↗

PubMed2002

Evolutionary and statistical properties of three genetic distances.

Many genetic distances have been developed to summarize allele frequency differences between populations. I review the evolutionary and statistical properties of three popular genetic distances: DS, DA, and theta;, using computer simulation of two simple evolutionary histories: an isolation model of population divergence and an equilibrium migration model. The effect of effective population size, mutation rate, and mutation mechanism upon the parametric value between pairs of populations in these models explored, and the unique properties of each distance are described. The effect of these evolutionary parameters on study design is also investigated and similar results are found for each genetic distance in each model of evolution: large sample sizes are warranted when populations are relatively genetically similar; and loci with more alleles produce better estimates of genetic distance.

Computer Simulation↗

PubMed2003

Opposites attract? Mate choice for parasite evasion and the evolutionary stability of sex.

If sex is naturally selected as a way to combat parasites, then sexual selection for disease resistance might increase the overall strength of selection for outcrossing. In the present study, we compared how two forms of mate choice affect the evolutionary stability of outcrossing in simultaneous hermaphrodites. In the first form, individuals preferred to mate with uninfected individuals (condition-dependent choice). In the second form, individuals preferred to mate with individuals that shared the least number of alleles in common at disease-resistance loci. The comparisons were made using individual-based computer simulations in which we varied parasite virulence, parasite transmission rate, and the rate of deleterious mutation at 500 viability loci. We found that alleles controlling both forms of mate choice spread when rare, but their effects on the evolutionary stability of sex were markedly different. Surprisingly, condition-dependent choice for uninfected mates had little effect on the evolutionary stability of sexual reproduction. In contrast, active choice for mates having different alleles at disease-resistance loci had a pronounced positive effect, especially under low rates of deleterious mutation. Based on these results, we suggest that mate choice that increases the genetic diversity of offspring can spread when rare in a randomly mating population, and, as an indirect consequence, increase the range of conditions under which sexual reproduction is evolutionarily stable.

Animals↗

PubMed2002

Is depression normal in human beings? A critique of the evolutionary perspective.

To the evolutionary biologist human beings at every stage of their development represent 'compromises' in their continual adaptation to their changing environments. Using a neo-Darwinian perspective, evolutionary psychiatrists such as Randolph Nesse (Professor of Psychiatry at the University of Michigan) argue that while natural selection does not shape disease itself, it does shape human traits and therefore vulnerability to disease. Accordingly, for him, depression is a human emotion which may represent a surviving positive response and is therefore not always pathological. This critique examines Nesse's principal arguments and reveals a number of weaknesses in those arguments. The article concludes with a review of the therapeutic and preventive implications of his evolutionary perspective on depressive states as well as some implications for mental health nurses.

Adaptation, Psychological↗

PubMed2000

An evolutionary approach to psychiatry.

OBJECTIVE: The current mainstream approach to psychiatry, characterised as empirical and phenomenological is questioned here and a new aetiological approach based on evolutionary theory is proposed. METHOD: A brief description of an evolutionary approach to animal behaviour is presented. The psychiatric states of anxiety, depression, 'hysterical' obsession and some aspects of psychosis are compared with related behaviours in other species. RESULTS: It is argued that this approach can be applied to psychiatric behaviour, that behavioural similarities exist between many psychiatric states and normal behaviour in species other than humans and many of these can be understood as adaptive. Some psychiatric states represent abnormally prominent adaptive behaviours, others represent distortions of these behaviours by a pathological process. An important line of thought in current animal behaviour research examines the concepts of self-awareness, consciousness, thought and affect in species other than man. These ideas, from an evolutionary perspective, are extended to psychiatry. A scheme illustrating this process is presented. CONCLUSIONS: We have drawn on relevant behavioural similarities between humans and other animals to show that many psychiatric states are distortions of evolved behaviour. The implications for classification, research and treatment are considerable. In particular this approach may form a bridge between fundamental research in molecular biology and the anthropomorphic approach of psychodynamics.

Adaptation, Psychological↗

PubMedDate not supplied

Analyzing evolutionary patterns in amniote embryonic development.

Heterochrony (differences in developmental timing between species) is a major mechanism of evolutionary change. However, the dynamic nature of development and the lack of a universal time frame makes heterochrony difficult to analyze. This has important repercussions in any developmental study that compares patterns of morphogenesis and gene expression across species. We describe a method that makes it possible to quantify timing shifts in embryonic development and to map their evolutionary history. By removing a direct dependence on traditional staging series, through the use of a relative time frame, it allows the analysis of developmental sequences across species boundaries. Applying our method to published data on vertebrate development, we identified clear patterns of heterochrony. For example, an early onset of various heart characters occurs throughout amniote evolution. This suggests that advanced (precocious) heart development arose in evolutionary history before endothermy. Our approach can be adapted to analyze other forms of comparative dynamic data, including patterns of developmental gene expression.

Age Factors↗