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PubMed2005

Phylogenetic perspectives in the evolution of parental care in ray-finned fishes.

Among major vertebrate groups, ray-finned fishes (Actinopterygii) collectively display a nearly unrivaled diversity of parental care activities. This fact, coupled with a growing body of phylogenetic data for Actinopterygii, makes these fishes a logical model system for analyzing the evolutionary histories of alternative parental care modes and associated reproductive behaviors. From an extensive literature review, we constructed a supertree for ray-finned fishes and used its phylogenetic topology to investigate the evolution of several key reproductive states including type of parental care (maternal, paternal, or biparental), internal versus external fertilization, internal versus external gestation, nest construction behavior, and presence versus absence of sexual dichromatism (as an indicator of sexual selection). Using a comparative phylogenetic approach, we critically evaluate several hypotheses regarding evolutionary pathways toward parental care. Results from maximum parsimony reconstructions indicate that all forms of parental care, including paternal, biparental, and maternal (both external and internal to the female reproductive tract) have arisen repeatedly and independently during ray-finned fish evolution. The most common evolutionary transitions were from external fertilization directly to paternal care and from external fertilization to maternal care via the intermediate step of internal fertilization. We also used maximum likelihood phylogenetic methods to test for statistical correlations and contingencies in the evolution of pairs of reproductive traits. Sexual dichromatism and nest construction proved to be positively correlated with the evolution of male parental care in species with external fertilization. Sexual dichromatism was also positively correlated with female-internal fertilization and gestation. No clear indication emerged that female-only care or biparental care were evolutionary outgrowths of male-only care, or that biparental care has been a common evolutionary stepping stone between paternal and maternal care. Results are discussed in the context of prior thought about the evolution of alternative parental care modes in vertebrates.

Animals↗

PubMed1989

Catechol stimulation of ferricyanide Hill reaction by spheroplasts of cyanobacterium, Synechococcus cedrorum: effect of temperature on catechol-stimulated oxygen evolution.

Catechol(o-dihydroxybenzene) at low concentrations (20-100 microM) stimulates FeCN-dependent O2 evolution of spheroplasts isolated from the cyanobacterium Synechococcus both in the presence and absence of DBMIB, an inhibitor of electron flow from PSII to PSI, the stimulation being two-fold with saturating concentration of (60 microM) catechol. Catechol thus appears to mediate the acceptance of electrons at the reducing side of PSII. Similarly it may act on the component of electron donor to PSII and caused the photoreduction of FeCN when O2 evolution capacity of spheroplasts is damaged by heat treatment. Analysis of the temperature effect on FeCN-supported O2 evolution by spheroplasts suggests that catechol shifts the temperature maxima to a lower temperature and thereby hastens the decay of O2 evolution capacity by heat as compared to the normal spheroplasts. Catechol also induces a change in the magnitude of activation energy for ferricyanide Hill activity of spheroplasts and lowers the transition temperature. These results suggest that lipophilic catechol brings about an alteration in membrane fluidity in cyanobacterial spheroplasts. Catechol is involved in a thermotropic destabilization of the membrane of the cyanobacterium. However, Al3+ was found to stabilize the membrane and raise the phase transition temperature. Further increase in temperature caused a gradual decline in the rate of O2 evolution.

Catechols↗

PubMedDate not supplied

[Effect of extra-intracranial microvascular anastomoses on the evolution of stenoses in the internal carotid artery system].

Clinical and angiographic examination of 20 patients with stenoses in the system of the internal carotid artery before and after operations for the formation of extra-intracranial microvascular anastomoses (EICMA), and during EICMA functioning demonstrated the evolution of the stenoses. It was characterized both by their increase (even up to the occurrence of thrombosis) and by their regression. No evolution of the stenoses occurred when EICMA failed to function. The character of evolution of the stenosis was determined by its localization. The trend of the evolution was dependent on the etiology of the stenosis. The degree of EICMA functioning differed and was determined by the character of stenosis evolution. With the development of stenosis into thrombosis, the neurological symptom complex was characterized both by marked augmentation followed by regression as well as by the absence of any changes or positive dynamics of the neurological changes.

Adolescent↗

PubMed1996

Independent evolution of the env and pol genes of HIV-1 during zidovudine therapy.

OBJECTIVE: To determine the effect that selection for antiviral resistance in the HIV-1 pol gene has on the level of variation and pattern of evolution in the V3 region of env. DESIGN: Proviral genomes obtained from two patients before, during and after the termination of zidovudine (ZDV) therapy (approximately 2 years) were amplified and sequenced in pol and env, and the evolution of the V3 hypervariable region compared with that of the reverse transcriptase domain of pol. METHODS: Gene fragments were polymerase chain reaction-amplified from patients' peripheral blood mononuclear cells. Nucleotide sequencing was carried out using T7 DNA polymerase and dye-labelled terminators on an automated DNA sequencer. Sequences were analysed using maximum likelihood phylogenetic techniques. RESULTS: Both patients showed multiple resistance-associated mutations after 1 year of ZDV therapy. Sequence diversity in V3 showed no reduction during the period of treatment. Substantial change continued to occur in this region and multiple lineages were present in both patients, in contrast to the single lineage observed in the pol gene of one (patient 74), a difference confirmed by likelihood ratio tests. CONCLUSIONS: There is no evidence from this study that selection due to antivirals has any significant impact on the evolution of the env gene. The independence in the evolution of these genes implies that recombination was occurring between the two genes during the study period. Such independent evolution should be allowed for in developing strategies for HIV therapy involving multiple target genes.

Amino Acid Sequence↗

PubMed2001

Molecular evolution of aerobic energy metabolism in primates.

As part of our goal to reconstruct human evolution at the DNA level, we have been examining changes in the biochemical machinery for aerobic energy metabolism. We find that protein subunits of two of the electron transfer complexes, complex III and complex IV, and cytochrome c, the protein carrier that connects them, have all undergone a period of rapid protein evolution in the anthropoid lineage that ultimately led to humans. Indeed, subunit IV of cytochrome c oxidase (COX; complex IV) provides one of the best examples of positively selected changes of any protein studied. The rate of subunit IV evolution accelerated in our catarrhine ancestors in the period between 40 to 18 million years ago and then decelerated in the descendant hominid lineages, a pattern of rate changes indicative of positive selection of adaptive changes followed by purifying selection acting against further changes. Besides clear evidence that adaptive evolution occurred for cytochrome c and subunits of complexes III (e.g., cytochrome c(1)) and IV (e.g., COX2 and COX4), modest rate accelerations in the lineage that led to humans are seen for other subunits of both complexes. In addition the contractile muscle-specific isoform of COX subunit VIII became a pseudogene in an anthropoid ancestor of humans but appears to be a functional gene in the nonanthropoid primates. These changes in the aerobic energy complexes coincide with the expansion of the energy-dependent neocortex during the emergence of the higher primates. Discovering the biochemical adaptations suggested by molecular evolutionary analysis will be an exciting challenge.

Animals↗

PubMed2025

Bacterial directed evolution of CRISPR base editors.

Base editing and other precision editing agents have transformed the utility and therapeutic potential of CRISPR-based genome editing. While some native enzymes edit efficiently with their nature-derived function, many enzymes require rational engineering or directed evolution to enhance the compatibility with mammalian cell genome editing. While many methods of engineering and directed evolution exist, plate-based discrete evolution offers an ideal balance between ease of use and engineering power. Here, we describe a detailed method for the bacterial directed evolution of CRISPR base editors that compounds technical ease with flexibility of application.

Gene Editing↗

PubMed1999

Evolution of the carabid ground beetles.

The phylogenetic relationships of the carabid ground beetles have been estimated by analysing a large part of the ND5 gene sequences of more than 1,000 specimens consisting of the representative species and geographic races covering most of the genera and subgenera known in the world. From the phylogenetic analyses in conjunction with the mtDNA-based dating, a scenario of the establishment of the present habitats of the respective Japanese carabids has been constructed. The carabid diversification took place ca. 40 MYA as an explosive radiation of the major genera. During evolution, occasional small or single bangs also took place, sometimes accompanied by parallel morphological evolution in phylogenetically remote as well as close lineages. The existence of silent periods, in which few morphological changes took place, has been recognized during evolution. Thus, the carabid evolution is discontinuous, alternatively having a phase of rapid morphological change and a silent phase.

Animals↗

PubMedDate not supplied

How many processes are responsible for phenotypic evolution?

In addressing phenotypic evolution, this article reconsiders natural selection, random drift, developmental constraints, and internal selection in the new extended context of evolutionary developmental biology. The change of perspective from the "evolution of phenotypes" toward an "evolution of ontogenies" (evo-devo perspective) affects the reciprocal relationships among these different processes. Random drift and natural selection are sibling processes: two forms of post-productional sorting among alternative developmental trajectories, the former random, the latter nonrandom. Developmental constraint is a compound concept; it contains even some forms of natural ("external" and "internal") selection. A narrower definition ("reproductive constraints") is proposed. Internal selection is not a selection caused by an internal agent. It is a form of environment-independent selection depending on the level of the organism's internal developmental or functional coordination. Selection and constraints are the main deterministic processes in phenotypic evolution but they are not opposing forces. Indeed, they are continuously interacting processes of evolutionary change, but with different roles that should not be confused.

Alleles↗

PubMedDate not supplied

Molecular studies of hemichordate development: a key to understanding the evolution of bilateral animals and chordates.

Using the Hawaiian acorn worm, Ptychodera flava, we began molecular studies on the development of hemichordates, a phylum previously unstudied at this level. Here we review results garnered from the examination of a few specific genes selected to help understand the evolution of vertebrate structures. These studies suggest new ideas about the evolution of developmental mechanisms in the deuterostomes. In a seminal observation, we noted an unexpected zone of expression of the Brachyurygene in the early anterior embryonic ectoderm where the mouth will form. Typically, the Brachyury gene is closely linked to development of the notochord and is expressed around the blastopore and in the posterior mesoderm in most animals. This first expression of Brachyury at the blastopore may represent a regulatory program associated with organizing the original animal head and gut opening, as suggested by the expression of Brachyury during hypostome formation in hydra. We believe that the anterior expression of Brachyury in deuterostomes represents the cooption of the program for organizing the original animal gut opening to form the deuterostome mouth. Recent data from the trochophore larva of a polychaete show that an anterior zone of expression of Brachyury is produced in this protostome by splitting of the Brachyury field during the formation of a gut with a mouth and anus by the lateral fusion of the sides of the blastopore. The ability to initiate independently a secondary regulatory program to organize the new mouth leading to an anterior field of Brachyury expression may be a signal event in the evolution of the deuterostomes. We also noted that the P. flava homolog of T-brain/Eomes, a gene closely related by sequence and expression around the blastopore to Brachyury and associated with development of the vertebrate brain, also exhibits early posterior expression around the blastopore and a field of de novo anterior ectoderm expression during later embryogenesis. The tissue in the zone of de novo anterior ectoderm expression of Pf-Tbrain produces the apical organ, a larval neural structure that has been touted as an evolutionary precursor of the chordate dorsal brain. The gene regulatory mechanisms responsible for initiating the anterior zone of de novo expression of T-brain may represent a cooption to specify early neuroectoderm of the regulatory program evolved first to drive anterior Brachyury expression for deuterostome mouth formation. It will be interesting to examine the possibilities that an ability to initiate the de novo anterior expression of the program that includes T-brain may be a key event in the evolution of the developmental mechanisms leading to the chordate dorsal nervous system.

Animals↗

PubMed2005

Mimicking natural evolution in metallo-beta-lactamases through second-shell ligand mutations.

Metallo-beta-lactamases (MBLs) represent the latest generation of beta-lactamases. The structural diversity and broad substrate profile of MBLs allow them to confer resistance to most beta-lactam antibiotics. To explore the evolutionary potential of these enzymes, we have subjected the Bacillus cereus MBL (BcII) to a directed evolution scheme, which resulted in an increased hydrolytic efficiency toward cephalexin. A systematic study of the hydrolytic profile, substrate binding, and active-site features of the evolved lactamase reveal that directed evolution has shaped the active site by means of remote mutations to better hydrolyze cephalosporins with small, uncharged C-3 substituents. One of these mutations is found in related enzymes from pathogenic bacteria and is responsible for the increase in that enzyme's hydrolytic profile. The mutations lowered the activation energy of the rate-limiting step rather than improved the affinity of the enzyme toward these substrates. The following conclusions can be made: (i) MBLs are able to expand their substrate spectrum without sacrificing their inherent hydrolytic capabilities; (ii) directed evolution is able to mimic mutations that occur in nature; (iii) the metal-ligand strength is tuned by second-shell mutations, thereby influencing the catalytic efficiency; and (iv) changes in the position of the second Zn(II) ion in MBLs affect the substrate positioning in the active site. Overall, these results show that the evolution of enzymatic catalysis can take place by remote mutations controlling reactivity.

Amino Acid Substitution↗

PubMed2024

Evolution of homologous recombination rates across bacteria.

Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as "quasi-sexual." However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate-as a trait-remains to be accurately described. Here, we developed an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate-as a trait-is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.

Bacteria↗

PubMed2026

Cooperation and the evolution of bacterial niche breadth.

Bacteria exhibit varying niche breadths, with generalists thriving in diverse environments and specialists confined to specific habitats. Although genes for cooperative traits have been suggested to influence niche breadth evolution, their precise role remains unclear. We used a combination of phylogeny-based comparative methods to test causal hypotheses about the directionality of the relationship between genes for cooperation and bacterial niche breadth evolution across 25,785 species. Our results revealed 1) a positive correlation between the proportion of genes for cooperation and niche breadth; 2) genes for cooperation influenced niche breadth evolution, with a decreased proportion of such genes promoting niche contraction as the predominant evolutionary direction; and 3) genes for cooperation experience more frequent gain and loss within species rather than across species. These findings suggest a role of bacterial cooperation in influencing niche breadth evolution and maintaining the ecological versatility of bacteria. While our results are consistent with a simple relationship under the hypotheses tested, more complex causal scenarios are possible, including the role of factors that influence both cooperation and niche breadth.

Phylogeny↗

PubMed1995

Transcriptional noise and the evolution of gene number.

Several proposals are made to explain the apparent increase in complexity of certain lineages during evolution. The proposals (not made in this order) are: (1) that gene number is a valid measure of biological complexity; (2) that gene number has not increased continuously during evolution, but has risen in discrete steps; (3) that two of the biggest steps occurred at the transition from prokaryotes to eukaryotes and the transition from invertebrates to vertebrates; (4) that these steps were made possible by 'systemic' changes in the way that genetic information is managed in the genome; (5) that the ability to silence inappropriate promoters is the primary limitation on gene number; (6) that the invention of nucleosomes (and perhaps the nuclear membrane) facilitated the evolution of eukaryotes from prokaryotic ancestors; (7) that the spread of low density methylation throughout the genome facilitated the evolution of vertebrates from invertebrate ancestors.

Animals↗

PubMed1995

Evolution of the cell cycle.

Cell proliferation involves duplication of all cell constituents and their more-or-less equal segregation to daughter cells. It seems probable that the performance of primitive cell-like structures would have been dogged by poor duplication and segregation fidelity, and by parasitism. This favoured evolution of the genome and with it the distinction between 'genomic' components like chromosomes whose synthesis is periodic and most other 'functional' components whose synthesis is continuous. Eukaryotic cells evolved from bacterial ancestors whose fused genome was replicated from a single origin and whose means of segregating sister chromatids depended on fixing their identity at replication. Evolution of an endo- or cytoskeleton, initially as means of consuming other bacteria, eventually enabled evolution of the mitotic spindle and a new means of segregating sister chromatids whose replication could be initiated from multiple origins. In this primitive eukaryotic cell, S and M phases might have been triggered by activation of a single cyclin-dependent kinase whose destruction along with that of other proteins would have triggered anaphase. Mitotic non-disjunction would have greatly facilitated genomic expansion, now possible due to multiple origins, and thereby accelerated the tempo of evolution when permitted by environmental conditions.

Archaea↗

PubMed2006

Human development x: Explanation of macroevolution--top-down evolution materializes consciousness. The origin of metamorphosis.

In this paper, we first give a short discussion of the macroevolution viewing life as information-directed, complex, dynamic systems. On this basis, we give our explanation of the origin of life and discuss the top-down evolution of molecules, proteins, and macroevolution. We discuss these subjects according to our new holistic biological paradigm. In view of this, we discuss the macroevolution of the organism, the species, the biosphere, and human society. After this, we discuss the shift in evolution from natural selection to a new proposed process of nature called the "metamorphous top-down" evolution. We discuss the capability of the evolutionary shift to govern some of the processes that lead to the formation of new species. We discuss the mechanisms we think are behind this proposed shift in evolution and conclude that this event is able to explain the huge biological diversity of nature in combination with evolutionary natural selection. We also discuss this event of nature as an isolated, but integrated, part of the universe. We propose the most important genetic and biochemical process that we think is behind the evolutionary shift as a complicated symbiosis of mechanisms leading to metamorphosis in all biological individuals, from bacteria to humans. The energetic superorbital that manifests the consciousness governs all these processes through quantum chemical activity. This is the key to evolutionary shift through the consciousness, and we propose to call this process "adult human metamorphosis".

Animals↗

PubMed2001

Evolution of myrmecophytism in western Malesian Macaranga (Euphorbiaceae).

Plants inhabited by ants (myrmecophytes) have evolved in a diversity of tropical plant lineages. Macaranga includes approximately 300 paleotropical tree species; in western Malesia there are 26 myrmecophytic species that vary in morphological specializations for ant association. The origin and diversification of myrmecophytism in Macaranga was investigated using phylogenetic analyses of morphological and nuclear ITS DNA characters and studies of character evolution. Despite low ITS variation, the combined analysis resulted in a well-supported hypothesis of relationships. Mapping myrmecophytism on all most parsimonious trees resulting from the combined analysis indicated that the trait evolved independently between two and four times and was lost between one and three times (five changes). This hypothesis was robust when tested against trees constrained to have three or fewer evolutionary transformations, although increased taxon sampling for the ITS analysis is required to confirm this. Mapping morphological traits on the phylogeny indicated that myrmecophytism was not homologous among lineages; each independent origin involved a suite of different specializations for ant-plant association. There was no evidence that myrmecophytic traits underwent sequential change through evolution; self-hollowing domatia evolved independently from ant-excavated domatia, and different food-body production types evolved in different lineages. The multiple origins of myrmecophytism in Macaranga were restricted to one small, exclusively western Malesian lineage of an otherwise large and nonmyrmecophytic genus. Although the evolution of aggregated food-body production and the formation of domatia coincided with the evolution of myrmecophytism in all cases, several morphological, ecological, and biogeographic factors appear to have facilitated and constrained this radiation of ant-plants.

Animals↗

PubMed2004

Perspective: is human cultural evolution Darwinian? Evidence reviewed from the perspective of the Origin of Species.

The claim that human culture evolves through the differential adoption of cultural variants, in a manner analogous to the evolution of biological species, has been greeted with much resistance and confusion. Here we demonstrate that as compelling a case can now be made that cultural evolution has key Darwinian properties, as Darwin himself presented for biological evolution in The Origin of Species. Culture is shown to exhibit variation, competition, inheritance, and the accumulation of successive cultural modifications over time. Adaptation, convergence, and the loss or change of function can also be identified in culture. Just as Darwin knew nothing of genes or particulate inheritance, a case for Darwinian cultural evolution can be made irrespective of whether unitary cultural replicators exist or whether cultural transmission mechanisms are well understood.

Adaptation, Biological↗

PubMedDate not supplied

The influence of UV radiation on protistan evolution.

Ultraviolet radiation has provided an evolutionary challenge to life on Earth. Recent increases in surficial ultraviolet B fluxes have focused attention on the role of UV radiation in protistan ecology, cancer, and DNA damage. Exploiting this new wealth of data, I examine the possibility that ultraviolet radiation may have played a significant role in the evolution of the first eukaryotes, that is, protists. Protists probably arose well before the formation of a significant ozone shield, and thus were probably subjected to substantial ultraviolet A, ultraviolet B, and ultraviolet C fluxes early in their evolution. Evolution consists of the generation of heritable variations and the subsequent selection of these variants. Ultraviolet radiation has played a role both as a mutagen and as a selective agent. In its role as a mutagen, it may have been crucial in the origin of sex and as a driver of molecular evolution. As a selective agent, its influence has been broad. Discussed in this paper are the influence of ultraviolet radiation on biogeography, photosynthesis, and desiccation resistance.

Animals↗