Genomic evolution during a 10,000-generation experiment with bacteria

Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.

Evolution of foraging behavior in Drosophila by density-dependent selection

One of the rare examples of a single major gene underlying a naturally occurring behavioral polymorphism is the foraging locus of Drosophila melanogaster. Larvae with the rover allele, forR, have significantly longer foraging path lengths on a yeast paste than do those homozygous for the sitter allele, fors. These variants do not differ in general activity in the absence of food. The evolutionary significance of this polymorphism is not as yet understood. Here we examine the effect of high and low animal rearing densities on the larval foraging path-length phenotype and show that density-dependent natural selection produces changes in this trait. In three unrelated base populations the long path (rover) phenotype was selected for under high-density rearing conditions, whereas the short path (sitter) phenotype was selected for under low-density conditions. Genetic crosses suggested that these changes resulted from alterations in the frequency of the fors allele in the low-density-selected lines. Further experiments showed that density-dependent selection during the larval stage rather than the adult stage of development was sufficient to explain these results. Density-dependent mechanisms may be sufficient to maintain variation in rover and sitter behavior in laboratory populations.

Evolution of RNA editing in trypanosome mitochondria

Two different RNA editing systems have been described in the kinetoplast-mitochondrion of trypanosomatid protists. The first involves the precise insertion and deletion of U residues mostly within the coding regions of maxicircle-encoded mRNAs to produce open reading frames. This editing is mediated by short overlapping complementary guide RNAs encoded in both the maxicircle and the minicircle molecules and involves a series of enzymatic cleavage-ligation steps. The second editing system is a C34 to U34 modification in the anticodon of the imported tRNATrp, thereby permitting the decoding of the UGA stop codon as tryptophan. U-insertion editing probably originated in an ancestor of the kinetoplastid lineage and appears to have evolved in some cases by the replacement of the original pan-edited cryptogene with a partially edited cDNA. The driving force for the evolutionary fixation of these retroposition events was postulated to be the stochastic loss of entire minicircle sequence classes and their encoded guide RNAs upon segregation of the single kinetoplast DNA network into daughter cells at cell division. A large plasticity in the relative abundance of minicircle sequence classes has been observed during cell culture in the laboratory. Computer simulations provide theoretical evidence for this plasticity if a random distribution and segregation model of minicircles is assumed. The possible evolutionary relationship of the C to U and U-insertion editing systems is discussed.

Kinetic Analysis and Pollutant Evolution During Thermal Degradation of Printed Circuit Boards Considering the Effect of Metals

Paper submitted to the 7th International Symposium on Feedstock Recycling of Polymeric Materials (7th ISFR 2013), New Delhi, India, 23-26 October 2013.

Paleogene evolution of the External Betic Zone and geodynamic implications

Interdisciplinary studies combining field data (geological and tectonic mapping, lithostratigraphic reconstructions, lithofacies characterization, correlations and sampling) and laboratory analyses (biostratigraphy, chronostratigraphy, clay mineralogy and sandstone petrography) of eight Senonian-Paleogene successions from the Sierra de La Pila and Sierra de El Carche areas (Murcia province, SE Spain) belonging to the External Betic Zone are presented. Field evidence of tectonic activity (slumps, olistostromes, syn-genetic folds, lateral variability, changes in thicknesses, para- and unconformity boundaries, stratigraphic gaps, shallowing upward trends to emersion, etc.) was found in several Paleogene intervals. The results enable a better reconstruction of the stratigraphic architecture and chronostratigraphy of the Paleogene record, highlighting in particular: facies evolution, discontinuities, depositional sequences (Middle-Upper Maastrichtian, Upper Paleocene-Middle Eocene, Oligocene-Lower Aquitanian), environmental evolution (homogeneous conditions during the Late Cretaceous and successive realm diversification from platform to slope to basin) and correlations, along the Prebetic to Subbetic transition, which is a key sector to understand the northeastward variations of the South Iberian margin. A conclusive paleogeographic and geodynamic evolutionary model for the study area is proposed, hypothesizing that Paleogene compressive tectonics affected the eastern External Betic Zone. In addition, correlations with successions from the western External Betic Zone evidenced asynchronous deformation from east to west along the internalmost External Betic Zone. Moreover, a comparison with the external Tunisian Tell enables the recognition of similar sedimentarytectonic events, imposing new constraints in the Paleogene geodynamic reconstruction throughout the western Tethys.

Evolution of Outcrossing in Experimental Populations of Caenorhabditis elegans

Caenorhabditis elegans can reproduce exclusively by self-fertilization. Yet, males can be maintained in laboratory populations, a phenomenon that continues to puzzle biologists. In this study we evaluated the role of males in facilitating adaptation to novel environments. For this, we contrasted the evolution of a fitness component exclusive to outcrossing in experimental populations of different mating systems. We introgressed a modifier of outcrossing into a hybrid population derived from several wild isolates to transform the wild-type androdioecious mating system into a dioecious mating system. By genotyping 375 single-nucleotide polymorphisms we show that the two populations had similar standing genetic diversity available for adaptation, despite the occurrence of selection during their derivation. We then performed replicated experimental evolution under the two mating systems from starting conditions of either high or low levels of diversity, under defined environmental conditions of discrete non-overlapping generations, constant density at high population sizes (N = 10(4)), no obvious spatial structure and abundant food resources. During 100 generations measurements of sex ratios and male competitive performance showed: 1) adaptation to the novel environment; 2) directional selection on male frequency under androdioecy; 3) optimal outcrossing rates of 0.5 under androdioecy; 4) the existence of initial inbreeding depression; and finally 5) that the strength of directional selection on male competitive performance does not depend on male frequencies. Taken together, these results suggest that androdioecious males are maintained at intermediate frequencies because outcrossing is adaptive.

Evolution of thermokarst in East Siberian ice-rich permafrost

Thermokarst lakes and basins are major components of ice-rich permafrost landscapes in East Siberian coastal lowlands and are regarded as indicators of regional climatic changes. We investigate the temporal and spatial dynamics of a 7.5 km**2, partly drained thermokarst basin (alas) using field investigations, remote sensing, Geographic Information Systems (GIS), and sediment analyses. The evolution of the thermokarst basin proceeded in two phases. The first phase started at the Pleistocene/Holocene transition (13 to 12 ka BP) with the initiation of a primary thermokarst lake on the Ice Complex surface. The lake expanded and persisted throughout the early Holocene before it drained abruptly about 5.7 ka BP, thereby creating a > 20 m deep alas with residual lakes. The second phase (5.7 ka BP to present) is characterized by alternating stages of lower and higher thermokarst intensity within the alas that were mainly controlled by local hydrological and relief conditions and accompanied by permafrost aggradation and degradation. It included diverse concurrent processes like lake expansion and stepwise drainage, polygonal ice-wedge growth, and the formation of drainage channels and a pingo, which occurred in different parts of the alas. This more dynamic thermokarst evolution resulted in a complex modern thermokarst landscape. However, on the regional scale, the changes during the second evolutionary phase after drainage of the initial thermokarst lakes were less intense than the early Holocene extensive thermokarst development in East Siberian coastal lowlands as a result of a significant regional change to warmer and wetter climate conditions.

And the beak shall inherit - evolution in response to invasion

The increased demographic performance of biological invaders may often depend on their escape from specifically adapted enemies. Here we report that native taxa in colonized regions may swiftly evolve to exploit such emancipated exotic species because of selection caused by invaders. A native Australian true bug has expanded it host range to include a vine imported from tropical America that has become a serious environmental weed. Based on field comparisons and historical museum specimens, we show that over the past 30-40 years, seed feeding soapberry bugs have evolved 5-10% longer mouthparts, better suited to attack the forest-invading balloon vines, which have large fruits. Laboratory experiments show that these differences are genetically based, and result in a near-doubling of the rate at which seeds are attacked. Thus a native biota that initially permits invasion may rapidly respond in ways that ultimately facilitate control.

Piggery pond sludge as a nitrogen source for crops. 1. Mineral N supply estimated from laboratory incubations and field application of stockpiled and wet sludge

Piggery pond sludge (PPS) was applied, as-collected (Wet PPS) and following stockpiling for 12 months ( Stockpiled PPS), to a sandy Sodosol and clay Vertosol at sites on the Darling Downs of Queensland. Laboratory measures of N availability were carried out on unamended and PPS-amended soils to investigate their value in estimating supplementary N needs of crops in Australia's northern grains region. Cumulative net N mineralised from the long-term ( 30 weeks) leached aerobic incubation was described by a first-order single exponential model. The mineralisation rate constant (0.057/week) was not significantly different between Control and PPS treatments or across soil types, when the amounts of initial mineral N applied in PPS treatments were excluded. Potentially mineralisable N (N-o) was significantly increased by the application of Wet PPS, and increased with increasing rate of application. Application of Wet PPS significantly increased the total amount of inorganic N leached compared with the Control treatments. Mineral N applied in Wet PPS contributed as much to the total mineral N status of the soil as did that which mineralised over time from organic N. Rates of CO2 evolution during 30 weeks of aerobic leached incubation indicated that the Stockpiled PPS was more stabilised (19-28% of applied organic C mineralised) than the Wet PPS (35-58% of applied organic C mineralised), due to higher lignin content in the former. Net nitrate-N produced following 12 weeks of aerobic non-leached incubation was highly correlated with net nitrate-N leached during 12 weeks of aerobic incubation (R-2 = 0.96), although it was

Adaptive evolution of a key phytoplankton species to ocean acidification

Ocean acidification, the drop in seawater pH associated with the ongoing enrichment of marine waters with carbon dioxide from fossil fuel burning, may seriously impair marine calcifying organisms. Our present understanding of the sensitivity of marine life to ocean acidification is based primarily on short-term experiments, in which organisms are exposed to increased concentrations of CO2. However, phytoplankton species with short generation times, in particular, may be able to respond to environmental alterations through adaptive evolution. Here, we examine the ability of the world's single most important calcifying organism, the coccolithophore Emiliania huxleyi, to evolve in response to ocean acidification in two 500-generation selection experiments. Specifically, we exposed E. huxleyi populations founded by single or multiple clones to increased concentrations of CO2. Around 500 asexual generations later we assessed their fitness. Compared with populations kept at ambient CO2 partial pressure, those selected at increased partial pressure exhibited higher growth rates, in both the single- and multiclone experiment, when tested under ocean acidification conditions. Calcification was partly restored: rates were lower under increased CO2 conditions in all cultures, but were up to 50% higher in adapted compared with non-adapted cultures. We suggest that contemporary evolution could help to maintain the functionality of microbial processes at the base of marine food webs in the face of global change.

Seawater carbonate chemistry and growth, carbon acquisition, and species interaction of Antarctic phytoplankton species in a laboratory experiment

Despite the fact that ocean acidification is considered to be especially pronounced in the Southern Ocean, little is known about CO2-dependent physiological processes and the interactions of Antarctic phytoplankton key species. We therefore studied the effects of CO2 partial pressure (PCO2) (16.2, 39.5, and 101.3 Pa) on growth and photosynthetic carbon acquisition in the bloom-forming species Chaetoceros debilis, Pseudo-nitzschia subcurvata, Fragilariopsis kerguelensis, and Phaeocystis antarctica. Using membrane-inlet mass spectrometry, photosynthetic O2 evolution and inorganic carbon (Ci) fluxes were determined as a function of CO2 concentration. Only the growth of C. debilis was enhanced under high PCO2. Analysis of the carbon concentrating mechanism (CCM) revealed the operation of very efficient CCMs (i.e., high Ci affinities) in all species, but there were species-specific differences in CO2-dependent regulation of individual CCM components (i.e., CO2 and uptake kinetics, carbonic anhydrase activities). Gross CO2 uptake rates appear to increase with the cell surface area to volume ratios. Species competition experiments with C. debilis and P. subcurvata under different PCO2 levels confirmed the CO2-stimulated growth of C. debilis observed in monospecific incubations, also in the presence of P. subcurvata. Independent of PCO2, high initial cell abundances of P. subcurvata led to reduced growth rates of C. debilis. For a better understanding of future changes in phytoplankton communities, CO2-sensitive physiological processes need to be identified, but also species interactions must be taken into account because their interplay determines the success of a species.

Permeability evolution across carbonate hosted normal fault zones

Acknowledgements: The authors would like to thank Total E&P and BG Group for project funding and support, and the Industry Technology Facilitator for facilitating the collaborative development (grant number 3322PSD). The authors would also like to express their gratitude to the Aberdeen Formation Evaluation Society and the College of Physical Sciences at the University of Aberdeen for partial financial support. Raymi Castilla (Total E&P), Fabrizio Agosta and Cathy Hollis are also thanked for their constructive comments and suggestions to improve the standard of this manuscript as are John Still and Colin Taylor (University of Aberdeen) for technical assistance in the laboratory. Piero Gianolla is thanked for his editorial handling of the manuscript.

Biological and Physical Factors Affecting the Natural History and Evolution of Encapsulated Development

The evolution of reproductive strategies involves a complex calculus of costs and benefits to both parents and offspring. Many marine animals produce embryos packaged in tough egg capsules or gelatinous egg masses attached to benthic surfaces. While these egg structures can protect against environmental stresses, the packaging is energetically costly for parents to produce. In this series of studies, I examined a variety of ecological factors affecting the evolution of benthic development as a life history strategy. I used marine gastropods as my model system because they are incredibly diverse and abundant worldwide, and they exhibit a variety of reproductive and developmental strategies.

The first study examines predation on benthic egg masses. I investigated: 1) behavioral mechanisms of predation when embryos are targeted (rather than the whole egg mass); 2) the specific role of gelatinous matrix in predation. I hypothesized that gelatinous matrix does not facilitate predation. One study system was the sea slug Olea hansineensis, an obligate egg mass predator, feeding on the sea slug Haminoea vesicula. Olea fed intensely and efficiently on individual Haminoea embryos inside egg masses but showed no response to live embryos removed from gel, suggesting that gelatinous matrix enables predation. This may be due to mechanical support of the feeding predator by the matrix. However, Haminoea egg masses outnumber Olea by two orders of magnitude in the field, and each egg mass can contain many tens of thousands of embryos, so predation pressure on individuals is likely not strong. The second system involved the snail Nassarius vibex, a non-obligate egg mass predator, feeding on the polychaete worm Clymenella mucosa. Gel neither inhibits nor promotes embryo predation for Nassarius, but because it cannot target individual embryos inside an egg mass, its feeding is slow and inefficient, and feeding rates in the field are quite low. However, snails that compete with Nassarius for scavenged food have not been seen to eat egg masses in the field, leaving Nassarius free to exploit the resource. Overall, egg mass predation in these two systems likely benefits the predators much more than it negatively affects the prey. Thus, selection for environmentally protective aspects of egg mass production may be much stronger than selection for defense against predation.

In the second study, I examined desiccation resistance in intertidal egg masses made by Haminoea vesicula, which preferentially attaches its flat, ribbon-shaped egg masses to submerged substrata. Egg masses occasionally detach and become stranded on exposed sand at low tide. Unlike adults, the encased embryos cannot avoid desiccation by selectively moving about the habitat, and the egg mass shape has high surface-area-to-volume ratio that should make it prone to drying out. Thus, I hypothesized that the embryos would not survive stranding. I tested this by deploying individual egg masses of two age classes on exposed sand bars for the duration of low tide. After rehydration, embryos midway through development showed higher rates of survival than newly-laid embryos, though for both stages survival rates over 25% were frequently observed. Laboratory desiccation trials showed that >75% survival is possible in an egg mass that has lost 65% of its water weight, and some survival (<25%) was observed even after 83% water weight lost. Although many surviving embryos in both experiments showed damage, these data demonstrate that egg mass stranding is not necessarily fatal to embryos. They may be able to survive a far greater range of conditions than they normally encounter, compensating for their lack of ability to move. Also, desiccation tolerance of embryos may reduce pressure on parents to find optimal laying substrata.

The third study takes a big-picture approach to investigating the evolution of different developmental strategies in cone snails, the largest genus of marine invertebrates. Cone snail species hatch out of their capsules as either swimming larvae or non-dispersing forms, and their developmental mode has direct consequences for biogeographic patterns. Variability in life history strategies among taxa may be influenced by biological, environmental, or phylogenetic factors, or a combination of these. While most prior research has examined these factors singularly, my aim was to investigate the effects of a host of intrinsic, extrinsic, and historical factors on two fundamental aspects of life history: egg size and egg number. I used phylogenetic generalized least-squares regression models to examine relationships between these two egg traits and a variety of hypothesized intrinsic and extrinsic variables. Adult shell morphology and spatial variability in productivity and salinity across a species geographic range had the strongest effects on egg diameter and number of eggs per capsule. Phylogeny had no significant influence. Developmental mode in Conus appears to be influenced mostly by species-level adaptations and niche specificity rather than phylogenetic conservatism. Patterns of egg size and egg number appear to reflect energetic tradeoffs with body size and specific morphologies as well as adaptations to variable environments. Overall, this series of studies highlights the importance of organism-scale biotic and abiotic interactions in evolutionary patterns.

The ecology and evolution of invasive Potamopyrgus antipodarum in Australia

The spread of invasive organisms is one of the greatest threats to ecosystems and biodiversity worldwide. Understanding the evolutionary and ecological factors responsible for the transport, introduction, establishment and spread of invasive species will assist the development of control strategies. The New Zealand mudsnail, Potamopyrgus antipodarum (Gray 1843) (Gastropoda: Hydrobiidae), is a global freshwater invader, with populations established in Europe, Asia, the Americas and Australia. While sexual and asexual P. antipodarum coexist in the native range, invasive populations reproduce by parthenogenesis, producing dense populations that compete for resources with native species. Potamopyrgus antipodarum is a natural model system for the study of evolutionary and ecological processes underlying invasion. This thesis assesses the invasion history, genetic diversity and ecology of P. antipodarum in Australia, with particular focus on: a) potential source populations, b) distribution and structure of populations, and c) species traits related to the establishment, persistence and spread of invasive P. antipodarum. Genetic analyses were carried out on specimens collected for this study from New Zealand and Australia, along with existing museum samples. In combination with published data, the analyses revealed low genetic diversity among and within invasive populations in south-eastern Australia, relative to New Zealand populations. Phylogenetic relationships inferred from mitochondrial sequences indicated that the Australian populations belong to clades dominated by parthenogenetic haplotypes that are known to be present in Europe and the US. These ‘invasive clades’ are likely to originate from the North Island of New Zealand, and suggest a role for selection in determining genetic composition of invasive populations. The genotypic diversity of Australian P. antipodarum was low, with few, closely related clones distributed across south-eastern Australia. The pattern of clone distribution was not consistent with any assessed geographical or abiotic factors; instead a few, widely-distributed clones were present in high frequencies at most sites. Differences in clone frequencies were found, which may indicate differential success of clonal lineages. A range of traits have been proposed as facilitators of invasion success, and within-species variation in these traits can promote differential success of genotypes. Using laboratory-based experiments, the performance of the three most common Australian clones was tested across a suite of invasion-relevant traits. Ecologically-relevant variation in traits was found among the clones. These differences may have determined the spatial distribution of clones, and may continue to do so into the future. This thesis found that the P. antipodarum invasion of Australia is the result of few introductions of a small number of globally-invasive genotypes that vary in ecologically-relevant traits. From a source of considerable genetic diversity in the native range, very few genotypes have become invasive. Those that are invasive appear to be very successful at continental scales. These findings highlight a capacity in asexual invaders to successfully invade, and potentially adapt to, a broad range of ecosystems. The P. antipodarum invasion system is amenable to research using combinations of field-based studies, molecular and laboratory approaches, and is likely to yield significant, broadly-applicable insights into invasion.

Observations of turbulence within the surf and swash zone of a field-scale sandy laboratory beach

Current coastal-evolution models generally lack the ability to accurately predict bed level change in shallow (<~2 m) water, which is, at least partly, due to the preclusion of the effect of surface-induced turbulence on sand suspension and transport. As a first step to remedy this situation, we investigated the vertical structure of turbulence in the surf and swash zone using measurements collected under random shoaling and plunging waves on a steep (initially 1:15) field-scale sandy laboratory beach. Seaward of the swash zone, turbulence was measured with a vertical array of three Acoustic Doppler Velocimeters (ADVs), while in the swash zone two vertically spaced acoustic doppler velocimeter profilers (Vectrino profilers) were applied. The vertical turbulence structure evolves from bottom-dominated to approximately vertically uniform with an increase in the fraction of breaking waves to ~ 50%. In the swash zone, the turbulence is predominantly bottom-induced during the backwash and shows a homogeneous turbulence profile during uprush. We further find that the instantaneous turbulence kinetic energy is phase-coupled with the short-wave orbital motion under the plunging breakers, with higher levels shortly after the reversal from offshore to onshore motion (i.e. wavefront).