Digital evolution in time-dependent fitness landscapes

We study the response of populations of digital organisms that adapt to a time-varying (periodic) fitness landscape of two oscillating peaks. We corroborate in general predictions from quasi-species theory in dynamic landscapes, such as adaptation to the average fitness landscape at small periods (high frequency) and quasistatic adaptation at large periods (low frequency). We also observe adaptive phase shifts (time tags between a change in the fitness landscape and art adaptive change in the population) that indicate a low-pass filter effect, in agreement with existing theory,. Finally, we witness long-term adaptation to fluctuating environments not anticipated in previous theoretical work

A Genome-Wide Analysis Reveals Significant Overlap of Transcription and DNA Repair in Stationary Phase Yeast

The association between transcription and DNA repair is acknowledged as a player in the generation of mutations in a non-random fashion in prokaryotes and eukaryotes. Previous studies demonstrated that the transcription complex is capable of directing DNA repair to sites of transcription. This process is especially important to growth-arrested cells, in which many DNA repair capacities are diminished; it may also lead to mutations preferentially in transcribed genes. Using microarray analysis of growth-arrested yeast cultures, we demonstrated on a genomic scale, the co-localization of a DNA-turnover marker, indicative of DNA-repair-associated DNA synthesis, with genes persistently transcribed during stationary phase. This may serve as a clue regarding the non-random manner in which non-dividing cells may potentially mutate in the absence of replication, solely as a result of their inherent, transcriptional stress response

Genetic learning particle swarm optimization

Social learning in particle swarm optimization (PSO) helps collective efficiency, whereas individual reproduction in genetic algorithm (GA) facilitates global effectiveness. This observation recently leads to hybridizing PSO with GA for performance enhancement. However, existing work uses a mechanistic parallel superposition and research has shown that construction of superior exemplars in PSO is more effective. Hence, this paper first develops a new framework so as to organically hybridize PSO with another optimization technique for “learning.” This leads to a generalized “learning PSO” paradigm, the *L-PSO. The paradigm is composed of two cascading layers, the first for exemplar generation and the second for particle updates as per a normal PSO algorithm. Using genetic evolution to breed promising exemplars for PSO, a specific novel *L-PSO algorithm is proposed in the paper, termed genetic learning PSO (GL-PSO). In particular, genetic operators are used to generate exemplars from which particles learn and, in turn, historical search information of particles provides guidance to the evolution of the exemplars. By performing crossover, mutation, and selection on the historical information of particles, the constructed exemplars are not only well diversified, but also high qualified. Under such guidance, the global search ability and search efficiency of PSO are both enhanced. The proposed GL-PSO is tested on 42 benchmark functions widely adopted in the literature. Experimental results verify the effectiveness, efficiency, robustness, and scalability of the GL-PSO

The dynamic Eukaryote Genome: Evolution, mobile DNA, and the TE-Thrust hypothesis

The discovery of transposable elements (TEs) by Barbara McClintock in the 1940s, triggered a new dawning in the development of evolutionary theory. However, similar to Gregor Mendel’s development of the laws of heredity in the nineteenth century, it was a long time before the full significance of this discovery was appreciated. Nevertheless, by the beginning of the 21st century, the study and recognition of TEs as significant factors in evolution was well underway. However, many evolutionary biologists still choose to ignore them, to highlight the loss of fitness in some individuals caused by TEs, or concentrate on the supposed parasitic nature of TEs, and the diseases they cause. The major concept and theme of this thesis is that the ubiquitous and extremely ancient transposable elements are not merely “junk DNA” or “selfish parasites” but are instead ‘powerful facilitators of evolution’. They can create genomic dynamism, and cause genetic changes of great magnitude and variety in the genotypes and phenotypes of eukaryotic lineages. A large variety of data are presented supporting the theme of TEs as very significant forces in evolution. This concept is formalised into a hypothesis, the TE-Thrust hypothesis, which explicitly presents detail of how TEs can facilitate evolution. This hypothesis opens the way to explaining otherwise inexplicable aspects of evolution, such as the mismatch between the phyletic gradualism theory, and the punctuated equilibrium concept, which is based on the fossil record. Data from the studies of many metazoans are analysed, with a focus on the well studied mammals, especially the primates. Data from the seed plants are also included, with a strong focus on Darwin’s ‘abominable mystery’, the rapid origin, and the extraordinary success of the flowering plants. TEs are ubiquitous and many of them are extremely ancient, probably dating back to the origin of the eukaryotes, and some are also found in prokaryotes. TEs can build, sculpt and reformat genomes by both active and passive means. Active TE-Thrust is due to transpositions by members of the TE consortium, or their retrotransposition of retrocopy genes, or by new acquisitions of TEs, or by the endogenisation of retroviruses, and other similar phenomena. Major results of this are that the promoters carried by TEs can result in very significant alterations in gene expression, and that sequences from the TEs themselves can become exapted or domesticated as novel genes. TEs can also cause exon shuffling, possibly building novel genes. Passive TE-Thrust is due to large homogenous consortia of inactive TEs that can act passively by causing ectopic recombination, resulting in genomic deletions, duplications, and possibly karyotypic changes. TE-Thrust often works together with other facilitators of evolution, such as point mutations, which can occur in duplicated, or retrocopy genes, sometimes resulting in new functions for such genes. A major concept in the TE-Thrust hypothesis is that although TEs are sometimes harmful to individuals, and can lower the fitness of a population, they endow the lineage of that population with adaptive potential and evolutionary potential. These are extremes of a continuum of intra-genomic potential, and are not separate entities. This adaptive/evolutionary potential due to the presence and activities of the TE consortium of the genomes in a lineage, greatly enhance the future survival prospects of the lineage, and its ability to undergo evolutionary transitions, and/or to radiate into a clade of multiple divergent lineages. Lineages may acquire a TE consortium by new infiltrations of TEs, either by horizontal transposon transfer, de novo synthesis, or endogenisation of retroviruses. Lineages lacking an effective TE consortium are likely to lack adaptive/evolutionary potential and could fail to diversify, become “living fossils”, or even become extinct, as many lineages ultimately do. The opposite of extinction is the fecund radiation of lineages, and it is shown here that fecund species-rich lineages such as rodents (Order Rodentia) and bats (Order Chiroptera) and the angiosperms, are all well endowed with many viable active TEs. The Simian Primates which have undergone major evolutionary transitions are also well endowed with viable and periodically active TEs, and/or large homogenous populations of TEs. Data on the “living fossils” such as the coelacanth and the tuatara are very limited, but indicate a lack of new acquisitions of TEs, and/or the mutational decay of ancient TE families in their genomes. Lineages are often in stasis, but a new acquisition of TEs, or other factors such as stress, hybridisation, or whole genome duplications (especially in angiosperms) may trigger a major burst of activity in the TE consortium, resulting in an evolutionary punctuation event. The TE-Thrust hypothesis thus offers an explanation for the punctuated equilibrium, frequently observed in the fossil record. There are many other known facilitators of evolution, such as point mutations, whole genome duplications, changes in allele frequency, epigenetic changes, symbiosis, hybridisation, simple sequence repeats, karyotypic changes, drift in small populations, allopatric and sympatric reproductive isolation, co-evolution, environmental and ecological changes, and so on. In addition, there may be some as yet unknown facilitators of evolution. However, TEs usually make up between 20 to 80 percent of the genomes of eukaryotes, as against one or two percent of coding genes, and are known to be able to make genomic modifications (“mutations”) that cannot be made by other facilitators of evolution. TEs also come in many superfamilies, and in thousands of families, which make up the mobile DNA of the earth’s biota. It is apparent then that their influence on, and facilitation of, eukaryotic evolution has been very significant indeed. In this thesis data are presented, which indicate that these ubiquitous and extremely ancient TEs are powerful facilitators of change, essential to the evolution of the earth’s biota. The TE-Thrust hypothesis, when fully explored, developed, and tested, if confirmed, must result in an extension to the Modern Synthesis, or even become a part of a new paradigm of evolutionary theory

The meadow jumping mouse genome and transcriptome suggest mechanisms of hibernation [preprint]

Hibernating mammals exhibit medically relevant phenotypes, but the genetic basis of hibernation remains poorly understood. Using the meadow jumping mouse (Zapus hudsonius), we investigated the genetic underpinnings of hibernation by uniting experimental and comparative genomic approaches. We assembled a Z. hudsonius genome and identified widespread expression changes during hibernation in genes important for circadian rhythm, membrane fluidity, and cell cycle arrest. Tissue-specific gene expression changes during torpor encompassed Wnt signaling in the brain and structural and transport functions in the kidney brush border. Using genomes from the closely related Zapus oregonus (previously classified as Z. princeps) and leveraging a panel of hibernating and non-hibernating rodents, we found selective pressure on genes involved in feeding behavior, metabolism, and cell biological processes potentially important for function at low body temperature. Leptin stands out with elevated conservation in hibernating rodents, implying a role for this metabolic hormone in triggering fattening and hibernation. These findings illustrate that mammalian hibernation requires adaptation at all levels of organismal form and function and lay the groundwork for future study of hibernation phenotypes

Integrating Horizontal Gene Transfer and Common Descent to Depict Evolution and Contrast It with ‘‘Common Design

Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of life’s diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD1 as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking ‘‘common design’’ (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded

Differential morphology and jumping performance of newly metamorphosed frogs of the hybridogenetic Rana esculenta complex

Closely related clonal and sexual populations may coexist in spite of the theorized lower potential for the evolution of clonal genotypes. Water frogs of the Rana esculenta complex have hemiclonal inheritance but most populations coexist with one of the recombinant parental species. We examine whether hemiclonal lineages may counterbalance their limitations of genetic variability by the adoption of one or more non-exclusive mechanisms: the general-purpose genotype or the frozen niche-variation model. Three coexisting hemiclones of the hybrid R. esculenta (GUT1, GUT2, GUT3) and both parental species (syntopic R. lessonae and allopatric R. ridibunda) were raised at two larval densities to examine morphological traits affecting jumping performance at the time of metamorphosis and size-independent jumping ability tested at three temperatures. Hind leg length and body mass at metamorphosis, traits that explain most of the variance in jumping performance, differed across hemiclones of R. esculenta. Metamorphs of hemiclone GUT1 had the longest hindlimbs and were bigger than metamorphs of the other hemiclones at low larval density but not at high density. Size adjusted jumping performance exhibited a significant genotype by larval density interaction. Metamorphs of GUT1 showed maximal jumping performance when raised at low larval density but at high density metamorphs of GUT2 were the best jumpers. In addition, within particular traits, differences were found between hemiclones across densities. These results appear to be consistent with both frozen niche-variation model and the general-purpose genotype model. Comparison with parental species revealed syntopic R. lessonae was smaller than hemiclones at metamorphosis but conversely exhibited better size-adjusted jumping performance when raised at low larval density. Temperature affected size-adjusted jumping performance only for frogs raised at low larval density but not for those raised at high larval densities. There was no significant temperature by hemiclone interaction.Peer Reviewe

Molecular evolution of opsins, a gene responsible for sensing light, in scallops (Bivalvia: Pectinidae)

Genetic diversity can cause drastic effects on phenotypes and is commonly the result of a gene duplication event. Gene duplication and subsequent functional divergence of opsins, a G-protein coupled-receptor (GPCR), have played an important role in expanding photoreceptive capabilities of organisms by altering what wavelengths of light are absorbed by photoreceptors (spectral tuning). Relatively few studies have been devoted to exploring the role of opsin duplication and evolution in non-arthropod invertebrates, and even fewer have integrated all the potential genetic diversity of opsins. In this dissertation, I utilized the photosensory system of the scallop, a marine bivalve, to study the evolution and expansion of the genetically diverse opsins, and demonstrate the complicated nature of Gq-opsin diversification after gene duplication. First, I explored how opsin paralogs diversify in function and evolutionary fate by characterizing four rhabdomeric (Gq-protein coupled) opsins in the scallop, Argopecten irradians. Using a phylogenetic framework, I showed a pattern consistent with two rounds of duplication generating the four paralogous Gq-opsins in scallops. Differential expression of the four Gq-opsins across ocular and extra-ocular photosensitive tissues suggested that the Gq-opsins are used in different biological contexts in scallops, while protein modeling reveals variation in the amino acid composition, suggesting the four Gq-opsin paralogs may absorb different wavelengths of light. Second, I investigated how two Gq-opsin paralogs differentiate after a duplication event across the scallop family, Pectinidae. By comparing the rates of evolution between paralogous clades, I demonstrated both paralogs are under purifying selection, yet maintained at rates that are significantly different. I showed that one amino acid position, which is not considered a putative spectral tuning site, stands out as a strong candidate to explain the source of selection driving the difference in evolutionary rates. Finally, I discussed the current role of allelic variation in sensory systems and described how alleles are often discarded in studies of molecular evolution. I demonstrated the breadth of possible allelic variation within an individual and stressed the potential of cryptic genetic variation in the evolution of organisms by examining the allelic variation in Gq-opsins sampled across 34 bivalve species