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PubMed1999

Evolution of evolvability.

Genomic sequence data provide evidence for a common origin of life and for its evolution by genetic variation via mutation and recombination. This paper discusses the fundamental dialectic paradigm of evolution--stability versus variability--at the crossroads of molecular genetics, population genetics, ecology, and the emerging science of experimental evolution. Experimental evolution of molecules, viruses, and bacteria can be used not only to test some basic evolutionary hypotheses but also to create new organisms for applications in biotechnology, agriculture, and medicine.

Adaptation, Biological↗

PubMed2005

Tracking Alu evolution in New World primates.

BACKGROUND: Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World) primates. RESULTS: Branching patterns along an Alu sequence phylogeny indicate three major classes of platyrrhine-specific Alu sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; AluTa7, AluTa10, and AluTa15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of AluSc- and AluSp-type elements. This is a novel mode of origin for new Alu subfamilies. CONCLUSION: The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.

Alu Elements↗

PubMed2004

Evidence for widespread convergent evolution around human microsatellites.

Microsatellites are a major component of the human genome, and their evolution has been much studied. However, the evolution of microsatellite flanking sequences has received less attention, with reports of both high and low mutation rates and of a tendency for microsatellites to cluster. From the human genome we generated a database of many thousands of (AC)(n) flanking sequences within which we searched for common characteristics. Sequences flanking microsatellites of similar length show remarkable levels of convergent evolution, indicating shared mutational biases. These biases extend 25-50 bases either side of the microsatellite and may therefore affect more than 30% of the entire genome. To explore the extent and absolute strength of these effects, we quantified the observed convergence. We also compared homologous human and chimpanzee loci to look for evidence of changes in mutation rate around microsatellites. Most models of DNA sequence evolution assume that mutations are independent and occur randomly. Allowances may be made for sites mutating at different rates and for general mutation biases such as the faster rate of transitions over transversions. Our analysis suggests that these models may be inadequate, in that proximity to even very short microsatellites may alter the rate and distribution of mutations that occur. The elevated local mutation rate combined with sequence convergence, both of which we find evidence for, also provide a possible resolution for the apparently contradictory inferences of mutation rates in microsatellite flanking sequences.

Base Sequence↗

PubMed1994

Ecosystem theory of evolution and social ethics.

Ecosystem evolution is driven by general laws for open systems aiming at immortality (first genetical then also cultural) of its components. Evolutionary impulses spread downward from ecosystem disturbances to population strategies to genome structures (opposite to the upward causation of traditional theory). Environmental cycles work as winding engine pushing evolution a step further at each round. Natural selection is being slackened with time while memory elaborates to conscious level. General trend is from unsustained growth to stability, individuation, increased diversity, standing biomass to productivity to dead mass ratios. Progressive evolution is interrupted by biospheric crises, or backward developments. Human activities contribute to the latter while for sustainable existence it will be necessary to switch from the crisis to the progress scheme. Human morals are grounded in million years of pre-human and pre-historic human evolution. However to be taught by nature means to comply with its progressive rather than backward tendencies. Human history as a continuation of the animal history is a perpetual struggle against natural selections.

Biological Evolution↗

PubMed1998

Environmental hypotheses of hominin evolution.

The study of human evolution has long sought to explain major adaptations and trends that led to the origin of Homo sapiens. Environmental scenarios have played a pivotal role in this endeavor. They represent statements or, more commonly, assumptions concerning the adaptive context in which key hominin traits emerged. In many cases, however, these scenarios are based on very little if any data about the past settings in which early hominins lived. Several environmental hypotheses of human evolution are presented in this paper. Explicit test expectations are laid out, and a preliminary assessment of the hypotheses is made by examining the environmental records of Olduvai, Turkana, Olorgesailie, Zhoukoudian, Combe Grenal, and other hominin localities. Habitat-specific hypotheses have prevailed in almost all previous accounts of human adaptive history. The rise of African dry savanna is often cited as the critical event behind the development of terrestrial bipedality, stone toolmaking, and encephalized brains, among other traits. This savanna hypothesis has been countered recently by the woodland/forest hypothesis, which claims that Pliocene hominins had evolved in and were primarily attracted to closed habitats. The ideas that human evolution was fostered by cold habitats in higher latitudes or by seasonal variations in tropical and temperate zones also have their proponents. An alternative view, the variability selection hypothesis, states that large disparities in environmental conditions were responsible for important episodes of adaptive evolution. The resulting adaptations enhanced behavioral versatility and ultimately ecological diversity in the human lineage. Global environmental records for the late Cenozoic and specific records at hominin sites show the following: 1) early human habitats were subject to large-scale remodeling over time; 2) the evidence for environmental instability does not support habitat-specific explanations of key adaptive changes; 3) the range of environmental change over time was more extensive and the tempo far more prolonged than allowed by the seasonality hypothesis; and 4) the variability selection hypothesis is strongly supported by the persistence of hominins through long sequences of environmental remodeling and the origin of important adaptations in periods of wide habitat diversity. Early bipedality, stone transport, diversification of artifact contexts, encephalization, and enhanced cognitive and social functioning all may reflect adaptations to environmental novelty and highly varying selective contexts.

Adaptation, Physiological↗

PubMed1998

Heterochronic processes in human evolution: an ontogenetic analysis of the hominid pelvis.

Changes in pelvic shape in human ontogeny and hominid phylogeny suggest that the heterochronic processes involved differ greatly from the neotenic process traditionally described in the evolution of the skull. The morphology of 150 juvenile and adult pelves of African apes, 60 juvenile and adult pelves of modern humans, two adult pelves and a juvenile hip bone of australopithecines (Sts 14, AL 288, MLD 7) was studied. Multivariate results, ontogenetic allometries, and growth curves confirm that the pelvic growth pattern in humans differs markedly from those of the African apes. The results permit the following conclusions. First, the appearance of a new feature (acetabulo-cristal buttress and cristal tubercle) at the time of human birth allows the addition of traits, such as the attainment of a proportionally narrower pelvis, with more sagittally positioned iliac blades. Pelvic proportions and orientation change progressively in early childhood as bipedalism is practiced. Other changes in pelvic proportions occur later with the adolescent growth spurt. Second, comparison of juvenile and adult australopithecines to modern humans indicates that 1) some pelvic traits of adult Australopithecus resemble those of neonate Homo; 2) the pelvic growth of Australopithecus was probably closer to that of apes, than to that of humans; and 3) prolonged growth in length of hindlimb and pelvis after sexual maturity seems to be a unique feature of Homo. The position of the acetabulo-cristal buttress and of the cristal tubercle on the ilium are similar in adult Australopithecus and neonate Homo suggesting that this feature may have been displaced later during hominid evolution. Progressive displacement of the acetabulo-cristal buttress on the ilium occurs both during hominid evolution (from Australopithecus to Homo sapiens) and human growth (from neonate to adult). This suggests peramorphic evolution of the pelvic morphology of hominids combining three processes of recapitulation (pre-displacement, acceleration and time hypermorphosis). The results lend credence to the hypothesis that no single heterochronic process accounts for all human evolutionary change; rather this reflects a combination of relative changes in growth rhythm and duration, including other perturbations, such as the appearance of new morphological features.

Adolescent↗

PubMed1998

The posterior border of the sphenoid greater wing and its phylogenetic usefulness in human evolution.

The elucidation of patterns of cranial skeletal maturation and growth in fossil hominids is possible not only through dental studies but also by mapping different aspects of ossification in both extant African apes and humans. However, knowledge of normal skeletal development in large samples of extant great apes is flimsy. To remedy this situation, this paper offers an extensive survey and thorough discussion of the ossification of the posterior border of the sphenoid greater wing. Indeed, this area provides much information about basicranial skeletal maturation. We investigate three variants: the absence of the foramen spinosum and the position of both the foramen spinosum and the foramen ovale in relation to the sphenosquamosal suture. Providing original data about humans and 1,425 extant great ape skulls and using a sample of 64 fossil hominids, this study aimed to test whether different ossification patterns occurred during the course of human evolution. The incidence of three derived morphologies located on the posterior border of the sphenoid greater wing increases during human evolution at different geological periods. The evolutionary polarity of these three derived morphologies is assessed by outgroup comparison and ontogenetic methods. During human evolution, there is a clear trend for the foramen spinosum to be present and wholly located on the posterior area of the sphenoid greater wing. Moreover, in all the great ape species and in Australopithecus afarensis, the sphenosquamosal suture may split the foramen ovale. Inversely, the foramen ovale always lies wholly within the sphenoid greater wing in Australopithecus africanus, robust australopithecines, early Homo, H. erectus (and/or H. ergaster), and Homo sapiens. From ontogenetic studies in humans, we conclude that, during human evolution, the ossification of the posterior area of the sphenoid greater wing progressively surrounded the middle meningeal artery (passing through the foramen spinosum) and the small meningeal artery (passing through the foramen ovale).

Animals↗

PubMed2001

Developmental mechanisms of vertebrate limb evolution.

Over the past few years, our understanding of the evolution of limbs has been improved by important new discoveries in the fossil record. Additionally, rapid progress has been made in identifying the molecular basis of vertebrate limb development. It is now possible to integrate these two areas of research in order to identify the molecular developmental mechanisms underlying the evolution of paired appendages in vertebrates. After the origin of paired appendages, several vertebrate lineages reduced or eliminated fins and limbs and returned to the limbless condition. Examples include eels, caecilians, snakes, slow worms and several marine mammals. Analyses of fossil and extant vertebrates show that evolution of limblessness frequently occurred together with elongation of the trunk and loss of clear morphological boundaries in the vertebral column. This may be suggestive of a common developmental mechanism linking these two processes. We have addressed this question by analysing python embryonic development at tissue, cellular and molecular levels, and we have identified a developmental mechanism which may account for evolution of limb loss in these animals.

Animals↗

PubMed2001

Structure and expression of the transthyretin gene in the choroid plexus: a model for the study of the mechanism of evolution.

Thyroid hormones are key regulators of brain differentiation and function. They permeate strongly into lipid membranes. However, a substantial portion of thyroid hormone is retained in the intravascular/extracellular compartments by binding to plasma proteins. In the brain, transthyretin is the most important of these proteins. This transthyretin is synthesized in the epithelial cells of the choroid plexus and exclusively secreted towards the brain. A net movement of thyroid hormones from the blood to the brain ensues. During evolution, transthyretin synthesis in the choroid plexus and the beginnings of a neocortex first appeared at the stage of the stem reptiles. The affinity of transthyretin for thyroxine increased and that for triiodothyronine decreased during evolution. This could augment the importance of deiodination for regulation of metabolism and gene expression by thyroid hormones in the brain. Successive shifts of the splice site at the 5' end of exon 2 of transthyretin precursor mRNA in the 3' direction led to a shortening of the N-terminal sections and to an increase in hydrophilicity of the N-terminal regions of transthyretin. This shift can be explained by a sequence of single base mutations. It could be an example for a molecular mechanism of positive Darwinian evolution. The selection pressure, which led to the expression of the transthyretin gene in the choroid plexus during evolution, might have been the maintenance of thyroid hormone homeostasis in the extracellular compartment of the brain in the presence of the greatly increasing volume of the lipid phase.

Amino Acid Sequence↗

PubMed2000

The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes.

The pyridoxal-5-phosphate-dependent enzymes (B6 enzymes) that act on amino acid substrates are of multiple evolutionary origin. The numerous common mechanistic features of B6 enzymes thus are not historical traits passed on from a common ancestor enzyme but rather reflect evolutionary or chemical necessities. Family profile analysis of amino acid sequences supported by comparison of the available three-dimensional (3-D) crystal structures indicates that the B6 enzymes known to date belong to four independent evolutionary lineages of homologous (or more precisely paralogous) proteins, of which the alpha family is by far the largest. The alpha family (with aspartate aminotransferase as the prototype enzyme) includes enzymes that catalyze, with several exceptions, transformations of amino acids in which the covalency changes are limited to the same carbon atom that carries the amino group forming the imine linkage with the coenzyme (i.e., Calpha in most cases). Enzymes of the beta family (tryptophan synthase beta as the prototype enzyme) mainly catalyze replacement and elimination reactions at Cbeta. The D-alanine aminotransferase family and the alanine racemase family are the two other independent lineages, both with relatively few member enzymes. The primordial pyridoxal-5-phosphate-dependent enzymes apparently were regio-specific catalysts that first diverged into reaction-specific enzymes and then specialized for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages. Comparison of sequences from eukaryotic, archebacterial, and eubacterial species indicates that the functional specialization of most B6 enzymes has occurred already in the universal ancestor cell. The cofactor pyridoxal-5-phosphate must have emerged very early in biological evolution; conceivably, organic cofactors and metal ions were the first biological catalysts. In attempts to stimulate particular steps of molecular evolution, oligonucleotide-directed mutagenesis of active-site residues and directed molecular evolution have been applied to change both the substrate and reaction specificity of existent B6 enzymes. Pyridoxal-5-phosphate-dependent catalytic antibodies were elicited with a screening protocol that applied functional selection criteria as they might have been operative in the evolution of protein-assisted pyridoxal catalysis.

Alanine Racemase↗

PubMed1999

Generation, integration, autonomy: three steps in the evolution of homology.

The homology concept harbours implicit assumptions about the evolution of morphological organization. Homologues are natural units in the construction of organismal body plans. Their origin and maintenance should represent a key element of a comprehensive theory of morphological evolution. Therefore, it is necessary to understand the causation of homology and to investigate the mechanisms underlying its origination. The study of this issue cannot be limited to the molecular level, because there appears to exist no strict correspondence between genetic and morphological evolution. It is argued that the establishment of homology follows three distinct (if overlapping) steps: (a) the generation of morphological building elements; (b) the integration of new elements into a body plan; and (c) the autonomization of integrated construction units as lineage-specific homologues of phenotypic evolution. In contrast with traditional views, it is proposed that the mechanistic basis for steps (a) and (b) is largely epigenetic, i.e. a consequence of the inherent propensities of developmental system under changing conditions. Step (c) transcends the proximate mechanisms underlying the establishment of homologues and makes them independent attractors of morphological organization at the phenotypic level.

Anatomy, Comparative↗

PubMed2007

A structure-centric view of protein evolution, design, and adaptation.

Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent in the indispensability of proteins for living cells is the fact that a given protein can adopt a specific three-dimensional shape that is specified solely by the protein's sequence of amino acids. Over the past several decades, structural biologists have demonstrated that the array of structures that proteins may adopt is quite astounding, and this has lead to a strong interest in understanding how protein structures change and evolve over time. In this review we consider a large body of recent work that attempts to illuminate this structure-centric picture of protein evolution. Much of this work has focused on the question of how completely new protein structures (i.e., new folds or topologies) are discovered by protein sequences as they evolve. Pursuant to this question of structural innovation has been a desire to describe and understand the observation that certain types of protein structures are far more abundant than others and how this uneven distribution of proteins implicates on the process through which new shapes are discovered. We consider a number of theoretical models that have been successful at explaining this heterogeneity in protein populations and discuss the increasing amount of evidence that indicates that the process of structural evolution involves the divergence of protein sequences and structures from one another. We also consider the topic of protein designability, which concerns itself with understanding how a protein's structure influences the number of sequences that can fold successfully into that structure. Understanding and quantifying the relationship between the physical feature of a structure and its designability has been a long-standing goal of the study of protein structure and evolution, and we discuss a number of recent advances that have yielded a promising answer to this question. Finally, we review the relatively new field of protein structural phylogeny, an area of study in which information about the distribution of protein structures among different organisms is used to reconstruct the evolutionary relationships between them. Taken together, the work that we review presents an increasingly coherent picture of how these unique polymers have evolved over the course of life on Earth.

Adaptation, Biological↗

PubMed2003

Evolution of a pigmentation gene, the melanocortin-1 receptor, in primates.

The melanocortin-1 receptor (MC1R) forms a critical switch in the production of orange/red pheomelanin and black/brown eumelanin pigments during hair development in mammals. The molecular evolution of the melanocortin-1 receptor gene was investigated in a broad range of primate species, including several groups with large differences in distribution of orange/red and black hairs. Primate MC1R has been subject to purifying selection throughout most of its evolution, with small changes in selective constraint being detected early in primate evolution. In contrast to the situation in humans and domestic mammals, many intraspecific and intrageneric differences in primate coat color cannot be attributed to changes in the MC1R coding sequence. Nevertheless, important changes in the biochemical function of MC1R are suggested by mutations in sites of known functional importance, particularly in New World monkeys and lemurs. The evolution of the MC1R in lion tamarins is anomalous, with a combination of a high nonsynonymous to synonymous substitution rate (dN/dS) ratio, deletions, and substitutions.

Adaptation, Physiological↗

PubMed2002

Functional evolution of Hox proteins in arthropods.

It is presumed that the evolution of morphological diversity in animals and plants is driven by changes in the developmental processes that govern morphology, hence basically by changes in the function and/or expression of a defined set of genes that control these processes. A large body of evidence has suggested that changes in developmental gene regulation are the predominant mechanisms that sustain morphological evolution, being much more important than the evolution of the primary sequences and functions of proteins. Recent reports challenge this idea by highlighting functional evolution of Hox proteins during the evolutionary history of arthropods.

Animals↗

PubMed2004

Recombination in HIV and the evolution of drug resistance: for better or for worse?

The rapid evolution of drug resistance remains a major obstacle for HIV therapy. The capacity of the virus for recombination is widely believed to facilitate the evolution of drug resistance. Here, we challenge this intuitive view. We develop a population genetic model of HIV replication that incorporates the processes of mutation, cellular superinfection, and recombination. We show that cellular superinfection increases the abundance of low fitness viruses at the expense of the fittest strains due to the mixing of viral proteins during virion assembly. Moreover, we argue that whether recombination facilitates the evolution of drug resistance depends critically on how resistance mutations interact to determine viral fitness. Contrary to the commonly held belief, we find that, under the most plausible biological assumptions, recombination is expected to slow down the rate of evolution of multi-drug-resistant virus during therapy.

Drug Resistance, Viral↗

PubMed2004

Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.

Recently, the first investigation of nucleoli using mass spectrometry led to the identification of 271 proteins. This represents a rich resource for a comprehensive investigation of nucleolus evolution. We applied a protocol for the identification of known and novel conserved protein domains of the nucleolus, resulting in the identification of 115 known and 91 novel domain profiles. The phyletic distribution of nucleolar protein domains in a collection of complete proteomes of selected organisms from all domains of life confirms the archaebacterial origin of the core machinery for ribosome maturation and assembly, but also reveals substantial eubacterial and eukaryotic contributions to nucleolus evolution. We predict that, in different phases of nucleolus evolution, protein domains with different biochemical functions were recruited to the nucleolus. We suggest a model for the late and continuous evolution of the nucleolus in early eukaryotes and argue against an endosymbiotic origin of the nucleolus and the nucleus. Supplementary material for this article can be found on the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html.

Archaeal Proteins↗

PubMed2005

How to get ahead: the origin, evolution and function of bicoid.

In Drosophila, a Bcd protein gradient orchestrates patterning along the anteroposterior embryonic axis. However, studies of basal flies and other insects have revealed that bcd is a derived Hox3 gene found only in higher dipterans. To understand how bcd acquired its role in flies and how anteroposterior patterning mechanisms have evolved, I first review key features of bcd function in Drosophila: anterior localization and transcriptional and translation control of gene expression. I then discuss investigations of bcd in other higher dipterans that have provided insight into the evolution of regulatory interactions and the Bcd gradient. Finally, I review studies of Drosophila and other insects that address the evolution of bcd function and integration of bcd into ancestral regulatory mechanisms. I suggest further comparative studies may allow us to identify the intermediate steps in bcd evolution. This will make bcd a paradigm for the origin and evolution of genes and regulatory networks.

Animals↗

PubMed1994

Molecular evolution: codes, clocks, genes and genomes.

The discoveries, advancements and continuing controversies in the field of molecular evolution are reviewed. Topics summarized are (1) the evolution of the genetic code, (2) gene evolution including the demonstration of homology, estimation of sequence divergence, phylogenetic trees, the molecular clock and the origin of genes and gene families by various genetic mechanisms, and (3) eukaryotic genome evolution, including the highly repeated satellite sequences, the interspersed and potentially mobile repeated sequences and the unique sequence fraction of the genome.

Biological Evolution↗