Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution

PubMed Central

2012-01-01

Background Chromosomal inversions have been pervasive during the evolution of the genus Drosophila, but there is significant variation between lineages in the rate of rearrangement fixation. D. mojavensis, an ecological specialist adapted to a cactophilic niche under extreme desert conditions, is a chromosomally derived species with ten fixed inversions, five of them not present in any other species. Results In order to explore the causes of the rapid chromosomal evolution in D. mojavensis, we identified and characterized all breakpoints of seven inversions fixed in chromosome 2, the most dynamic one. One of the inversions presents unequivocal evidence for its generation by ectopic recombination between transposon copies and another two harbor inverted duplications of non-repetitive DNA at the two breakpoints and were likely generated by staggered single-strand breaks and repair by non-homologous end joining. Four out of 14 breakpoints lay in the intergenic region between preexisting duplicated genes, suggesting an adaptive advantage of separating previously tightly linked duplicates. Four out of 14 breakpoints are associated with transposed genes, suggesting these breakpoints are fragile regions. Finally two inversions contain novel genes at their breakpoints and another three show alterations of genes at breakpoints with potential adaptive significance. Conclusions D. mojavensis chromosomal inversions were generated by multiple mechanisms, an observation that does not provide support for increased mutation rate as explanation for rapid chromosomal evolution. On the other hand, we have found a number of gene alterations at the breakpoints with putative adaptive consequences that directly point to natural selection as the cause of D. mojavensis rapid chromosomal evolution. PMID:22296923

No evidence for faster male hybrid sterility in population crosses of an intertidal copepod (Tigriopus californicus).

PubMed

Willett, Christopher S

2008-06-01

Two different forces are thought to contribute to the rapid accumulation of hybrid male sterility that has been observed in many inter-specific crosses, namely the faster male and the dominance theories. For male heterogametic taxa, both faster male and dominance would work in the same direction to cause the rapid evolution of male sterility; however, for taxa lacking differentiated sex chromosomes only the faster male theory would explain the rapid evolution of male hybrid sterility. It is currently unknown what causes the faster evolution of male sterility, but increased sexual selection on males and the sensitivity of genes involved in male reproduction are two hypotheses that could explain the observation. Here, patterns of hybrid sterility in crosses of genetically divergent copepod populations are examined to test potential mechanisms of faster male evolution. The study species, Tigriopus californicus, lacks differentiated, hemizygous sex chromosomes and appears to have low levels of divergence caused by sexual selection acting upon males. Hybrid sterility does not accumulate more rapidly in males than females in these crosses suggesting that in this taxon male reproductive genes are not inherently more prone to disruption in hybrids.

Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature.

PubMed

Ghalambor, Cameron K; Hoke, Kim L; Ruell, Emily W; Fischer, Eva K; Reznick, David N; Hughes, Kimberly A

2015-09-17

Phenotypic plasticity is the capacity for an individual genotype to produce different phenotypes in response to environmental variation. Most traits are plastic, but the degree to which plasticity is adaptive or non-adaptive depends on whether environmentally induced phenotypes are closer or further away from the local optimum. Existing theories make conflicting predictions about whether plasticity constrains or facilitates adaptive evolution. Debate persists because few empirical studies have tested the relationship between initial plasticity and subsequent adaptive evolution in natural populations. Here we show that the direction of plasticity in gene expression is generally opposite to the direction of adaptive evolution. We experimentally transplanted Trinidadian guppies (Poecilia reticulata) adapted to living with cichlid predators to cichlid-free streams, and tested for evolutionary divergence in brain gene expression patterns after three to four generations. We find 135 transcripts that evolved parallel changes in expression within the replicated introduction populations. These changes are in the same direction exhibited in a native cichlid-free population, suggesting rapid adaptive evolution. We find 89% of these transcripts exhibited non-adaptive plastic changes in expression when the source population was reared in the absence of predators, as they are in the opposite direction to the evolved changes. By contrast, the remaining transcripts exhibiting adaptive plasticity show reduced population divergence. Furthermore, the most plastic transcripts in the source population evolved reduced plasticity in the introduction populations, suggesting strong selection against non-adaptive plasticity. These results support models predicting that adaptive plasticity constrains evolution, whereas non-adaptive plasticity potentiates evolution by increasing the strength of directional selection. The role of non-adaptive plasticity in evolution has received relatively little attention; however, our results suggest that it may be an important mechanism that predicts evolutionary responses to new environments.

Plant domestication slows pest evolution.

PubMed

Turcotte, Martin M; Lochab, Amaneet K; Turley, Nash E; Johnson, Marc T J

2015-09-01

Agricultural practices such as breeding resistant varieties and pesticide use can cause rapid evolution of pest species, but it remains unknown how plant domestication itself impacts pest contemporary evolution. Using experimental evolution on a comparative phylogenetic scale, we compared the evolutionary dynamics of a globally important economic pest - the green peach aphid (Myzus persicae) - growing on 34 plant taxa, represented by 17 crop species and their wild relatives. Domestication slowed aphid evolution by 13.5%, maintained 10.4% greater aphid genotypic diversity and 5.6% higher genotypic richness. The direction of evolution (i.e. which genotypes increased in frequency) differed among independent domestication events but was correlated with specific plant traits. Individual-based simulation models suggested that domestication affects aphid evolution directly by reducing the strength of selection and indirectly by increasing aphid density and thus weakening genetic drift. Our results suggest that phenotypic changes during domestication can alter pest evolutionary dynamics. © 2015 John Wiley & Sons Ltd/CNRS.

Rapid evolution meets invasive species control: The potential for pesticide resistance in sea lamprey

USGS Publications Warehouse

Dunlop, Erin S.; McLaughlin, Robert L.; Adams, Jean V.; Jones, Michael L.; Birceanu, Oana; Christie, Mark R.; Criger, Lori A.; Hinderer, Julia L.M.; Hollingworth, Robert M.; Johnson, Nicholas; Lantz, Stephen R.; Li, Weiming; Miller, James R.; Morrison, Bruce J.; Mota-Sanchez, David; Muir, Andrew M.; Sepulveda, Maria S.; Steeves, Todd B.; Walter, Lisa; Westman, Erin; Wirgin, Isaac; Wilkie, Michael P.

2018-01-01

Rapid evolution of pest, pathogen and wildlife populations can have undesirable effects; for example, when insects evolve resistance to pesticides or fishes evolve smaller body size in response to harvest. A destructive invasive species in the Laurentian Great Lakes, the sea lamprey (Petromyzon marinus) has been controlled with the pesticide 3-trifluoromethyl-4-nitrophenol (TFM) since the 1950s. We evaluated the likelihood of sea lamprey evolving resistance to TFM by (1) reviewing sea lamprey life history and control; (2) identifying physiological and behavioural resistance strategies; (3) estimating the strength of selection from TFM; (4) assessing the timeline for evolution; and (5) analyzing historical toxicity data for evidence of resistance. The number of sea lamprey generations exposed to TFM was within the range observed for fish populations where rapid evolution has occurred. Mortality from TFM was estimated as 82-90%, suggesting significant selective pressure. However, 57 years of toxicity data revealed no increase in lethal concentrations of TFM. Vigilance and the development of alternative controls are required to prevent this aquatic invasive species from evolving strategies to evade control.

Initial Dynamical Evolution of Star Clusters with Tidal Field

NASA Astrophysics Data System (ADS)

Park, So-Myoung; Goodwin, Simon P.; Kim, Sungsoo S.

2017-03-01

Observations have been suggested that star clusters could form from the rapid collapse and violent relaxation of substructured distributions. We investigate the collapse of fractal stellar distributions in no, weak, and very strong tidal fields. We find that the rapid collapse of substructure into spherical clusters happens quickly with no or a weak tidal field, but very strong tidal fields prevent a cluster forming. However, we also find that dense Plummer spheres are also rapidly destroyed in strong tidal fields. We suggest that this is why the low-mass star clusters cannot survive near the galactic centre which has strong tidal field.

Life history tradeoffs in cancer evolution

PubMed Central

Boddy, Amy M.; Gatenby, Robert A.; Brown, Joel S.; Maley, Carlo C.

2014-01-01

Somatic evolution during cancer progression and therapy results in tumor cells that exhibit a wide range of phenotypes including rapid proliferation and quiescence. Evolutionary life history theory may help us understand the diversity of these phenotypes. Fast life history organisms reproduce rapidly while those with slow life histories show less fecundity and invest more resources in survival. Life history theory also provides an evolutionary framework for phenotypic plasticity with potential implications for understanding ‘cancer stem cells’. Life history theory suggests that different therapy dosing schedules could select for fast or slow life history cell phenotypes, with important clinical consequences. PMID:24213474

Rapid evolution and copy number variation of primate RHOXF2, an X-linked homeobox gene involved in male reproduction and possibly brain function.

PubMed

Niu, Ao-lei; Wang, Yin-qiu; Zhang, Hui; Liao, Cheng-hong; Wang, Jin-kai; Zhang, Rui; Che, Jun; Su, Bing

2011-10-12

Homeobox genes are the key regulators during development, and they are in general highly conserved with only a few reported cases of rapid evolution. RHOXF2 is an X-linked homeobox gene in primates. It is highly expressed in the testicle and may play an important role in spermatogenesis. As male reproductive system is often the target of natural and/or sexual selection during evolution, in this study, we aim to dissect the pattern of molecular evolution of RHOXF2 in primates and its potential functional consequence. We studied sequences and copy number variation of RHOXF2 in humans and 16 nonhuman primate species as well as the expression patterns in human, chimpanzee, white-browed gibbon and rhesus macaque. The gene copy number analysis showed that there had been parallel gene duplications/losses in multiple primate lineages. Our evidence suggests that 11 nonhuman primate species have one RHOXF2 copy, and two copies are present in humans and four Old World monkey species, and at least 6 copies in chimpanzees. Further analysis indicated that the gene duplications in primates had likely been mediated by endogenous retrovirus (ERV) sequences flanking the gene regions. In striking contrast to non-human primates, humans appear to have homogenized their two RHOXF2 copies by the ERV-mediated non-allelic recombination mechanism. Coding sequence and phylogenetic analysis suggested multi-lineage strong positive selection on RHOXF2 during primate evolution, especially during the origins of humans and chimpanzees. All the 8 coding region polymorphic sites in human populations are non-synonymous, implying on-going selection. Gene expression analysis demonstrated that besides the preferential expression in the reproductive system, RHOXF2 is also expressed in the brain. The quantitative data suggests expression pattern divergence among primate species. RHOXF2 is a fast-evolving homeobox gene in primates. The rapid evolution and copy number changes of RHOXF2 had been driven by Darwinian positive selection acting on the male reproductive system and possibly also on the central nervous system, which sheds light on understanding the role of homeobox genes in adaptive evolution.

Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster.

PubMed

Burke, Molly K; Barter, Thomas T; Cabral, Larry G; Kezos, James N; Phillips, Mark A; Rutledge, Grant A; Phung, Kevin H; Chen, Richard H; Nguyen, Huy D; Mueller, Laurence D; Rose, Michael R

2016-09-01

Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes.

PubMed

Newton, Matilda S; Arcus, Vickery L; Patrick, Wayne M

2015-06-06

The evolution of enzymes is often viewed as following a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. In this review, we summarize experimental data that suggest a different reality. Modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid. Experiments to infer and resurrect ancient sequences suggest that some of the first organisms present on the Earth are likely to have possessed highly active enzymes. Reconciling these observations, we argue that rapid bursts of strong selection for increased catalytic efficiency are interspersed with much longer periods in which the catalytic power of an enzyme erodes, through neutral drift and selection for other properties such as cellular energy efficiency or regulation. Thus, many enzymes may have already passed their catalytic peaks. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Retroviruses facilitate the rapid evolution of the mammalian placenta

PubMed Central

Chuong, Edward B.

2015-01-01

The mammalian placenta exhibits elevated expression of endogenous retroviruses (ERVs), but the evolutionary significance of this feature remains unclear. I propose that ERV-mediated regulatory evolution was, and continues to be, an important mechanism underlying the evolution of placenta development. Many recent studies have focused on the co-option of ERV-derived genes for specific functional adaptations in the placenta. However, the co-option of ERV-derived regulatory elements has the potential to co-opt entire gene regulatory networks, which, I argue, would facilitate relatively rapid developmental evolution of the placenta. I suggest a model in which an ancient retroviral infection led to the establishment of the ancestral placental developmental gene network through the co-option of ERV-derived regulatory elements. Consequently, placenta development would require elevated tolerance to ERV activity, which in turn would expose a continuous stream of novel ERV mutations that may have catalyzed the developmental diversification of the mammalian placenta. PMID:23873343

Evolution under changing climates: climatic niche stasis despite rapid evolution in a non-native plant.

PubMed

Alexander, Jake M

2013-09-22

A topic of great current interest is the capacity of populations to adapt genetically to rapidly changing climates, for example by evolving the timing of life-history events, but this is challenging to address experimentally. I use a plant invasion as a model system to tackle this question by combining molecular markers, a common garden experiment and climatic niche modelling. This approach reveals that non-native Lactuca serriola originates primarily from Europe, a climatic subset of its native range, with low rates of admixture from Asia. It has rapidly refilled its climatic niche in the new range, associated with the evolution of flowering phenology to produce clines along climate gradients that mirror those across the native range. Consequently, some non-native plants have evolved development times and grow under climates more extreme than those found in Europe, but not among populations from the native range as a whole. This suggests that many plant populations can adapt rapidly to changed climatic conditions that are already within the climatic niche space occupied by the species elsewhere in its range, but that evolution to conditions outside of this range is more difficult. These findings can also help to explain the prevalence of niche conservatism among non-native species.

Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

ERIC Educational Resources Information Center

Delpech, Roger

2009-01-01

This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

Evidence of Repeated and Independent Saltational Evolution in a Peculiar Genus of Sphinx Moths (Proserpinus: Sphingidae)

PubMed Central

Rubinoff, Daniel; Le Roux, Johannes J.

2008-01-01

Background Saltational evolution in which a particular lineage undergoes relatively rapid, significant, and unparalleled change as compared with its closest relatives is rarely invoked as an alternative model to the dominant paradigm of gradualistic evolution. Identifying saltational events is an important first-step in assessing the importance of this discontinuous model in generating evolutionary novelty. We offer evidence for three independent instances of saltational evolution in a charismatic moth genus with only eight species. Methodology/Principal Findings Maximum parsimony, maximum likelihood and Bayesian search criteria offered congruent, well supported phylogenies based on 1,965 base pairs of DNA sequence using the mitochondrial gene cytochrome oxidase subunit I, and the nuclear genes elongation factor-1 alpha and wingless. Using a comparative methods approach, we examined three taxa exhibiting novelty in the form of Batesian mimicry, host plant shift, and dramatic physiological differences in light of the phylogenetic data. All three traits appear to have evolved relatively rapidly and independently in three different species of Proserpinus. Each saltational species exhibits a markedly different and discrete example of discontinuous trait evolution while remaining canalized for other typical traits shared by the rest of the genus. All three saltational taxa show insignificantly different levels of overall genetic change as compared with their congeners, implying that their divergence is targeted to particular traits and not genome-wide. Conclusions/Significance Such rapid evolution of novel traits in individual species suggests that the pace of evolution can be quick, dramatic, and isolated—even on the species level. These results may be applicable to other groups in which specific taxa have generated pronounced evolutionary novelty. Genetic mechanisms and methods for assessing such relatively rapid changes are postulated. PMID:19107205

Evidence of repeated and independent saltational evolution in a peculiar genus of sphinx moths (Proserpinus: Sphingidae).

PubMed

Rubinoff, Daniel; Le Roux, Johannes J

2008-01-01

Saltational evolution in which a particular lineage undergoes relatively rapid, significant, and unparalleled change as compared with its closest relatives is rarely invoked as an alternative model to the dominant paradigm of gradualistic evolution. Identifying saltational events is an important first-step in assessing the importance of this discontinuous model in generating evolutionary novelty. We offer evidence for three independent instances of saltational evolution in a charismatic moth genus with only eight species. Maximum parsimony, maximum likelihood and Bayesian search criteria offered congruent, well supported phylogenies based on 1,965 base pairs of DNA sequence using the mitochondrial gene cytochrome oxidase subunit I, and the nuclear genes elongation factor-1 alpha and wingless. Using a comparative methods approach, we examined three taxa exhibiting novelty in the form of Batesian mimicry, host plant shift, and dramatic physiological differences in light of the phylogenetic data. All three traits appear to have evolved relatively rapidly and independently in three different species of Proserpinus. Each saltational species exhibits a markedly different and discrete example of discontinuous trait evolution while remaining canalized for other typical traits shared by the rest of the genus. All three saltational taxa show insignificantly different levels of overall genetic change as compared with their congeners, implying that their divergence is targeted to particular traits and not genome-wide. Such rapid evolution of novel traits in individual species suggests that the pace of evolution can be quick, dramatic, and isolated--even on the species level. These results may be applicable to other groups in which specific taxa have generated pronounced evolutionary novelty. Genetic mechanisms and methods for assessing such relatively rapid changes are postulated.

Rapid Birth-and-Death Evolution of Imprinted snoRNAs in the Prader-Willi Syndrome Locus: Implications for Neural Development in Euarchontoglires

PubMed Central

Zhang, Yi-Jun; Yang, Jian-Hua; Shi, Qiao-Su; Zheng, Ling-Ling; Liu, Jun; Zhou, Hui; Zhang, Hui; Qu, Liang-Hu

2014-01-01

Imprinted small nucleolar RNAs (snoRNAs) are only found in eutherian genomes and closely related to brain functions. A complex human neurological disease, Prader-Willi syndrome (PWS), is primarily attributed to the deletion of imprinted snoRNAs in chromosome 15q11-q13. Here we investigated the snoRNA repertoires in the PWS locus of 12 mammalian genomes and their evolution processes. A total of 613 imprinted snoRNAs were identified in the PWS homologous loci and the gene number was highly variable across lineages, with a peak in Euarchontoglires. Lineage-specific gene gain and loss events account for most extant genes of the HBII-52 (SNORD115) and the HBII-85 (SNORD116) gene family, and remarkable high gene-birth rates were observed in the primates and the rodents. Meanwhile, rapid sequence substitution occurred only in imprinted snoRNA genes, rather than their flanking sequences or the protein-coding genes located in the same imprinted locus. Strong selective constraints on the functional elements of these imprinted snoRNAs further suggest that they are subjected to birth-and-death evolution. Our data suggest that the regulatory role of HBII-52 on 5-HT2CR pre-mRNA might originate in the Euarchontoglires through adaptive process. We propose that the rapid evolution of PWS-related imprinted snoRNAs has contributed to the neural development of Euarchontoglires. PMID:24945811

Rapid Evolution of the Gaseous Exoplanetary Debris around the White Dwarf Star HE 1349–2305

NASA Astrophysics Data System (ADS)

Dennihy, E.; Clemens, J. C.; Dunlap, B. H.; Fanale, S. M.; Fuchs, J. T.; Hermes, J. J.

2018-02-01

Observations of heavy metal pollution in white dwarf stars indicate that metal-rich planetesimals are frequently scattered into star-grazing orbits, tidally disrupted, and accreted onto the white dwarf surface, offering direct insight into the dynamical evolution of post-main-sequence exoplanetary systems. Emission lines from the gaseous debris in the accretion disks of some of these systems show variations on timescales of decades, and have been interpreted as the general relativistic precession of a recently formed, elliptical disk. Here we present a comprehensive spectroscopic monitoring campaign of the calcium infrared triplet emission in one system, HE 1349–2305, which shows morphological emission profile variations suggestive of a precessing, asymmetric intensity pattern. The emission profiles are shown to vary on a timescale of one to two years, which is an order of magnitude shorter than what has been observed in other similar systems. We demonstrate that this timescale is likely incompatible with general relativistic precession, and consider alternative explanations for the rapid evolution, including the propagation of density waves within the gaseous debris. We conclude with recommendations for follow-up observations, and discuss how the rapid evolution of the gaseous debris in HE 1349–2305 could be leveraged to test theories of exoplanetary debris disk evolution around white dwarf stars.

Evolution of human immunodeficiency virus type 1 in perinatally infected infants with rapid and slow progression to disease.

PubMed Central

Salvatori, F; Masiero, S; Giaquinto, C; Wade, C M; Brown, A J; Chieco-Bianchi, L; De Rossi, A

1997-01-01

We addressed the relationship between the origin and evolution of human immunodeficiency virus type 1 (HIV-1) variants and disease outcome in perinatally infected infants by studying the V3 regions of viral variants in samples obtained from five transmitting mothers at delivery and obtained sequentially over the first year of life from their infected infants, two of whom (rapid progressors) rapidly progressed to having AIDS. Phylogenetic analyses disclosed that the V3 sequences from each mother-infant pair clustered together and were clearly distinct from those of the other pairs. Within each pair, the child's sequences formed a monophyletic group, indicating that a single variant initiated the infection in both rapid and slow progressors. Plasma HIV-1 RNA levels increased in all five infants during their first months of life and then declined within the first semester of life only in the three slow progressors. V3 variability increased over time in all infants, but no differences in the pattern of V3 evolution in terms of potential viral phenotype were observed. The numbers of synonymous and nonsynonymous substitutions varied during the first semester of life regardless of viral load, CD4+-cell count, and disease progression. Conversely, during the second semester of life the rate of nonsynonymous substitutions was higher than that of synonymous substitutions in the slow progressors but not in the rapid progressors, thus suggesting a stronger host selective pressure in the former. In view of the proposal that V3 genetic evolution is driven mainly by host immune constraints, these findings suggest that while the immune response to V3 might contribute to regulating viral levels after the first semester of life, it is unlikely to play a determinant role in the initial viral decline soon after birth. PMID:9151863

Biophysics, environmental stochasticity, and the evolution of thermal safety margins in intertidal limpets.

PubMed

Denny, M W; Dowd, W W

2012-03-15

As the air temperature of the Earth rises, ecological relationships within a community might shift, in part due to differences in the thermal physiology of species. Prediction of these shifts - an urgent task for ecologists - will be complicated if thermal tolerance itself can rapidly evolve. Here, we employ a mechanistic approach to predict the potential for rapid evolution of thermal tolerance in the intertidal limpet Lottia gigantea. Using biophysical principles to predict body temperature as a function of the state of the environment, and an environmental bootstrap procedure to predict how the environment fluctuates through time, we create hypothetical time-series of limpet body temperatures, which are in turn used as a test platform for a mechanistic evolutionary model of thermal tolerance. Our simulations suggest that environmentally driven stochastic variation of L. gigantea body temperature results in rapid evolution of a substantial 'safety margin': the average lethal limit is 5-7°C above the average annual maximum temperature. This predicted safety margin approximately matches that found in nature, and once established is sufficient, in our simulations, to allow some limpet populations to survive a drastic, century-long increase in air temperature. By contrast, in the absence of environmental stochasticity, the safety margin is dramatically reduced. We suggest that the risk of exceeding the safety margin, rather than the absolute value of the safety margin, plays an underappreciated role in the evolution of thermal tolerance. Our predictions are based on a simple, hypothetical, allelic model that connects genetics to thermal physiology. To move beyond this simple model - and thereby potentially to predict differential evolution among populations and among species - will require significant advances in our ability to translate the details of thermal histories into physiological and population-genetic consequences.

Exponential evolution: implications for intelligent extraterrestrial life.

PubMed

Russell, D A

1983-01-01

Some measures of biologic complexity, including maximal levels of brain development, are exponential functions of time through intervals of 10(6) to 10(9) yrs. Biological interactions apparently stimulate evolution but physical conditions determine the time required to achieve a given level of complexity. Trends in brain evolution suggest that other organisms could attain human levels within approximately 10(7) yrs. The number (N) and longevity (L) terms in appropriate modifications of the Drake Equation, together with trends in the evolution of biological complexity on Earth, could provide rough estimates of the prevalence of life forms at specified levels of complexity within the Galaxy. If life occurs throughout the cosmos, exponential evolutionary processes imply that higher intelligence will soon (10(9) yrs) become more prevalent than it now is. Changes in the physical universe become less rapid as time increases from the Big Bang. Changes in biological complexity may be most rapid at such later times. This lends a unique and symmetrical importance to early and late universal times.

Virus Satellites Drive Viral Evolution and Ecology

PubMed Central

Frígols, Belén; Quiles-Puchalt, Nuria; Mir-Sanchis, Ignacio; Donderis, Jorge; Elena, Santiago F.; Buckling, Angus; Novick, Richard P.; Marina, Alberto; Penadés, José R.

2015-01-01

Virus satellites are widespread subcellular entities, present both in eukaryotic and in prokaryotic cells. Their modus vivendi involves parasitism of the life cycle of their inducing helper viruses, which assures their transmission to a new host. However, the evolutionary and ecological implications of satellites on helper viruses remain unclear. Here, using staphylococcal pathogenicity islands (SaPIs) as a model of virus satellites, we experimentally show that helper viruses rapidly evolve resistance to their virus satellites, preventing SaPI proliferation, and SaPIs in turn can readily evolve to overcome phage resistance. Genomic analyses of both these experimentally evolved strains as well as naturally occurring bacteriophages suggest that the SaPIs drive the coexistence of multiple alleles of the phage-coded SaPI inducing genes, as well as sometimes selecting for the absence of the SaPI depressing genes. We report similar (accidental) evolution of resistance to SaPIs in laboratory phages used for Staphylococcus aureus typing and also obtain the same qualitative results in both experimental evolution and phylogenetic studies of Enterococcus faecalis phages and their satellites viruses. In summary, our results suggest that helper and satellite viruses undergo rapid coevolution, which is likely to play a key role in the evolution and ecology of the viruses as well as their prokaryotic hosts. PMID:26495848

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans.

PubMed

Shen, Tong; Xu, Shixia; Wang, Xiaohong; Yu, Wenhua; Zhou, Kaiya; Yang, Guang

2012-03-24

Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans.

Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

PubMed Central

2012-01-01

Background Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans. PMID:22443485

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations.

PubMed

Lenski, Richard E

2017-10-01

Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.

Long-term phenotypic evolution of bacteria.

PubMed

Plata, Germán; Henry, Christopher S; Vitkup, Dennis

2015-01-15

For many decades comparative analyses of protein sequences and structures have been used to investigate fundamental principles of molecular evolution. In contrast, relatively little is known about the long-term evolution of species' phenotypic and genetic properties. This represents an important gap in our understanding of evolution, as exactly these proprieties play key roles in natural selection and adaptation to diverse environments. Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. Overall, bacterial phenotypic evolution can be described by a two-stage process with a rapid initial phenotypic diversification followed by a slow long-term exponential divergence. The observed average divergence trend, with approximately similar fractions of phenotypic properties changing per unit time, continues for billions of years. We experimentally confirm the predicted divergence trend using the phenotypic profiles of 40 diverse bacterial species across more than 60 growth conditions. Our analysis suggests that, at long evolutionary distances, gene essentiality is significantly more conserved than the ability to utilize different nutrients, while synthetic lethality is significantly less conserved. We also find that although a rapid phenotypic evolution is sometimes observed within the same species, a transition from high to low phenotypic similarity occurs primarily at the genus level.

Sperm competition, immunity, selfish genes and cancer.

PubMed

Lewis, Z; Price, T A R; Wedell, N

2008-10-01

Sperm competition is widespread and has played an important role in shaping male reproductive characters such as testis size and numbers of sperm produced, and this is reflected in the rapid evolution of many reproductive genes. Additionally, sperm competition has been implicated in the rapid evolution of seminal fluids. However, our understanding of the molecular basis of many traits thought to be important in sperm competition is rudimentary. Furthermore, links between sperm competition and a range of issues not directly related to reproduction are only just beginning to be explored. These include associations between sperm competition and selfish genes, immunity and diseases such as cancer.We briefly review these topics and suggest areas we consider worthy of additional research.

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

PubMed

Krishnan, Arunkumar; Iyer, Lakshminarayan M; Holland, Stephen J; Boehm, Thomas; Aravind, L

2018-04-03

AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa. Copyright © 2018 the Author(s). Published by PNAS.

Evolution of reproductive proteins from animals and plants.

PubMed

Clark, Nathaniel L; Aagaard, Jan E; Swanson, Willie J

2006-01-01

Sexual reproduction is a fundamental biological process common among eukaryotes. Because of the significance of reproductive proteins to fitness, the diversity and rapid divergence of proteins acting at many stages of reproduction is surprising and suggests a role of adaptive diversification in reproductive protein evolution. Here we review the evolution of reproductive proteins acting at different stages of reproduction among animals and plants, emphasizing common patterns. Although we are just beginning to understand these patterns, by making comparisons among stages of reproduction for diverse organisms we can begin to understand the selective forces driving reproductive protein diversity and the functional consequences of reproductive protein evolution.

Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity.

PubMed

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-05-19

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi-piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts.

PubMed

Daugherty, Matthew D; Young, Janet M; Kerns, Julie A; Malik, Harmit S

2014-01-01

Post-translational protein modifications such as phosphorylation and ubiquitinylation are common molecular targets of conflict between viruses and their hosts. However, the role of other post-translational modifications, such as ADP-ribosylation, in host-virus interactions is less well characterized. ADP-ribosylation is carried out by proteins encoded by the PARP (also called ARTD) gene family. The majority of the 17 human PARP genes are poorly characterized. However, one PARP protein, PARP13/ZAP, has broad antiviral activity and has evolved under positive (diversifying) selection in primates. Such evolution is typical of domains that are locked in antagonistic 'arms races' with viral factors. To identify additional PARP genes that may be involved in host-virus interactions, we performed evolutionary analyses on all primate PARP genes to search for signatures of rapid evolution. Contrary to expectations that most PARP genes are involved in 'housekeeping' functions, we found that nearly one-third of PARP genes are evolving under strong recurrent positive selection. We identified a >300 amino acid disordered region of PARP4, a component of cytoplasmic vault structures, to be rapidly evolving in several mammalian lineages, suggesting this region serves as an important host-pathogen specificity interface. We also found positive selection of PARP9, 14 and 15, the only three human genes that contain both PARP domains and macrodomains. Macrodomains uniquely recognize, and in some cases can reverse, protein mono-ADP-ribosylation, and we observed strong signatures of recurrent positive selection throughout the macro-PARP macrodomains. Furthermore, PARP14 and PARP15 have undergone repeated rounds of gene birth and loss during vertebrate evolution, consistent with recurrent gene innovation. Together with previous studies that implicated several PARPs in immunity, as well as those that demonstrated a role for virally encoded macrodomains in host immune evasion, our evolutionary analyses suggest that addition, recognition and removal of ADP-ribosylation is a critical, underappreciated currency in host-virus conflicts.

Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts

PubMed Central

Daugherty, Matthew D.; Young, Janet M.; Kerns, Julie A.; Malik, Harmit S.

2014-01-01

Post-translational protein modifications such as phosphorylation and ubiquitinylation are common molecular targets of conflict between viruses and their hosts. However, the role of other post-translational modifications, such as ADP-ribosylation, in host-virus interactions is less well characterized. ADP-ribosylation is carried out by proteins encoded by the PARP (also called ARTD) gene family. The majority of the 17 human PARP genes are poorly characterized. However, one PARP protein, PARP13/ZAP, has broad antiviral activity and has evolved under positive (diversifying) selection in primates. Such evolution is typical of domains that are locked in antagonistic ‘arms races’ with viral factors. To identify additional PARP genes that may be involved in host-virus interactions, we performed evolutionary analyses on all primate PARP genes to search for signatures of rapid evolution. Contrary to expectations that most PARP genes are involved in ‘housekeeping’ functions, we found that nearly one-third of PARP genes are evolving under strong recurrent positive selection. We identified a >300 amino acid disordered region of PARP4, a component of cytoplasmic vault structures, to be rapidly evolving in several mammalian lineages, suggesting this region serves as an important host-pathogen specificity interface. We also found positive selection of PARP9, 14 and 15, the only three human genes that contain both PARP domains and macrodomains. Macrodomains uniquely recognize, and in some cases can reverse, protein mono-ADP-ribosylation, and we observed strong signatures of recurrent positive selection throughout the macro-PARP macrodomains. Furthermore, PARP14 and PARP15 have undergone repeated rounds of gene birth and loss during vertebrate evolution, consistent with recurrent gene innovation. Together with previous studies that implicated several PARPs in immunity, as well as those that demonstrated a role for virally encoded macrodomains in host immune evasion, our evolutionary analyses suggest that addition, recognition and removal of ADP-ribosylation is a critical, underappreciated currency in host-virus conflicts. PMID:24875882

CD4+ T-cell recovery with suppressive ART-induced rapid sequence evolution in hepatitis C virus envelope but not NS3.

PubMed

Liu, Lin; Nardo, David; Li, Eric; Wang, Gary P

2016-03-13

CD4 T-cell depletion from HIV infection leads to a global decline in anti-hepatitis C virus (HCV) envelope neutralizing antibody (nAb) response, which may play a role in accelerating liver fibrosis. An increase in anti-HCV nAb titers has been reported during antiretroviral therapy (ART) but its impact on HCV remains poorly understood. The objective of this study is to determine the effects of ART on long-term HCV evolution. We examined HCV quasispecies structure and long-term evolution in HIV/HCV coinfected patients with ART-induced CD4 T-cell recovery, and compared with patients with CD4 T-cell depletion from delayed ART. We applied a single-variant sequencing (SVS) method to construct authentic viral quasispecies and compared sequence evolution in HCV envelope, the primary target for humoral immune responses, and NS3, a target for cellular immunity, between the two cohorts. The SVS method corrected biases known to skew the proportions of viral variants, revealing authentic HCV quasispeices structures. We observed higher rates of HCV envelope sequence evolution in patients with ART-induced CD4 T-cell recovery, compared with patients with CD4 T-cell depletion from delayed ART (P = 0.03). Evolutionary rates for NS3 were considerably lower than the rates for envelope (P < 0.01), with no significant difference observed between the two groups. ART-induced CD4 T-cell recovery results in rapid sequence evolution in HCV envelope, but not in NS3. These results suggest that suppressive ART disproportionally enhances HCV-specific humoral responses more than cellular responses, resulting in rapid sequence evolution in HCV envelope but not NS3.

Correlated evolution between male ejaculate allocation and female remating behaviour in seed beetles (Bruchidae).

PubMed

Katvala, M; Rönn, J L; Arnqvist, G

2008-03-01

Sperm competition theory suggests that female remating rate determines the selective regime that dictates the evolution of male ejaculate allocation. To test for correlated evolution between female remating behaviour and male ejaculate traits, we subjected detailed experimental data on female and male reproductive traits in seven-seed beetle species to phylogenetic comparative analyses. The evolution of a larger first ejaculate was positively correlated with the evolution of a more rapid decline in ejaculate size over successive matings. Further, as predicted by theory, an increase in female remating rate correlated with the evolution of larger male testes but smaller ejaculates. However, an increase in female remating was associated with the evolution of a less even allocation of ejaculate resources over successive matings, contrary to classic sperm competition theory. We failed to find any evidence for coevolution between the pattern of male ejaculate allocation and variation in female quality and we conclude that some patterns of correlated evolution are congruent with current theory, whereas some are not. We suggest that this may reflect the fact that much sperm competition theory does not fully incorporate other factors that may affect the evolution of male and female traits, such as trade-offs between ejaculate expenditure and other competing demands and the evolution of resource acquisition.

Nearby galaxies as pointers to a better theory of cosmic evolution.

PubMed

Peebles, P J E; Nusser, Adi

2010-06-03

The great advances in the network of cosmological tests show that the relativistic Big Bang theory is a good description of our expanding Universe. However, the properties of nearby galaxies that can be observed in greatest detail suggest that a better theory would describe a mechanism by which matter is more rapidly gathered into galaxies and groups of galaxies. This more rapid growth occurs in some theoretical ideas now under discussion.

Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity

PubMed Central

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-01-01

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi–piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. PMID:24846630

Genomic linkage of male song and female acoustic preference QTL underlying a rapid species radiation

PubMed Central

Shaw, Kerry L.; Lesnick, Sky C.

2009-01-01

The genetic coupling hypothesis of signal-preference evolution, whereby the same genes control male signal and female preference for that signal, was first inspired by the evolution of cricket acoustic communication nearly 50 years ago. To examine this hypothesis, we compared the genomic location of quantitative trait loci (QTL) underlying male song and female acoustic preference variation in the Hawaiian cricket genus Laupala. We document a QTL underlying female acoustic preference variation between 2 closely related species (Laupala kohalensis and Laupala paranigra). This preference QTL colocalizes with a song QTL identified previously, providing compelling evidence for a genomic linkage of the genes underlying these traits. We show that both song and preference QTL make small to moderate contributions to the behavioral difference between species, suggesting that divergence in mating behavior among Laupala species is due to the fixation of many genes of minor effect. The diversity of acoustic signaling systems in crickets exemplifies the evolution of elaborate male displays by sexual selection through female choice. Our data reveal genetic conditions that would enable functional coordination between song and acoustic preference divergence during speciation, resulting in a behaviorally coupled mode of signal-preference evolution. Interestingly, Laupala exhibits one of the fastest rates of speciation in animals, concomitant with equally rapid evolution in sexual signaling behaviors. Genomic linkage may facilitate rapid speciation by contributing to genetic correlations between sexual signaling behaviors that eventually cause sexual isolation between diverging populations. PMID:19487670

Time-limited environments affect the evolution of egg-body size allometry.

PubMed

Eckerström-Liedholm, Simon; Sowersby, Will; Gonzalez-Voyer, Alejandro; Rogell, Björn

2017-07-01

Initial offspring size is a fundamental component of absolute growth rate, where large offspring will reach a given adult body size faster than smaller offspring. Yet, our knowledge regarding the coevolution between offspring and adult size is limited. In time-constrained environments, organisms need to reproduce at a high rate and reach a reproductive size quickly. To rapidly attain a large adult body size, we hypothesize that, in seasonal habitats, large species are bound to having a large initial size, and consequently, the evolution of egg size will be tightly matched to that of body size, compared to less time-limited systems. We tested this hypothesis in killifishes, and found a significantly steeper allometric relationship between egg and body sizes in annual, compared to nonannual species. We also found higher rates of evolution of egg and body size in annual compared to nonannual species. Our results suggest that time-constrained environments impose strong selection on rapidly reaching a species-specific body size, and reproduce at a high rate, which in turn imposes constraints on the evolution of egg sizes. In combination, these distinct selection pressures result in different relationships between egg and body size among species in time-constrained versus permanent habitats. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Rapid evolution of the cerebellum in humans and other great apes.

PubMed

Barton, Robert A; Venditti, Chris

2014-10-20

Humans' unique cognitive abilities are usually attributed to a greatly expanded neocortex, which has been described as "the crowning achievement of evolution and the biological substrate of human mental prowess". The human cerebellum, however, contains four times more neurons than the neocortex and is attracting increasing attention for its wide range of cognitive functions. Using a method for detecting evolutionary rate changes along the branches of phylogenetic trees, we show that the cerebellum underwent rapid size increase throughout the evolution of apes, including humans, expanding significantly faster than predicted by the change in neocortex size. As a result, humans and other apes deviated significantly from the general evolutionary trend for neocortex and cerebellum to change in tandem, having significantly larger cerebella relative to neocortex size than other anthropoid primates. These results suggest that cerebellar specialization was a far more important component of human brain evolution than hitherto recognized and that technical intelligence was likely to have been at least as important as social intelligence in human cognitive evolution. Given the role of the cerebellum in sensory-motor control and in learning complex action sequences, cerebellar specialization is likely to have underpinned the evolution of humans' advanced technological capacities, which in turn may have been a preadaptation for language. Copyright © 2014 Elsevier Ltd. All rights reserved.

Rapidity evolution of gluon TMD from low to moderate x

DOE PAGES

Balitsky, Ian; Tarasov, A.

2015-10-05

In this article, we study how the rapidity evolution of gluon transverse momentum dependent distribution changes from nonlinear evolution at smallmore » $$x \\ll 1$$ to linear evolution at moderate $$x \\sim 1$$.« less

Trophic specialization drives morphological evolution in sea snakes.

PubMed

Sherratt, Emma; Rasmussen, Arne R; Sanders, Kate L

2018-03-01

Viviparous sea snakes are the most rapidly speciating reptiles known, yet the ecological factors underlying this radiation are poorly understood. Here, we reconstructed dated trees for 75% of sea snake species and quantified body shape (forebody relative to hindbody girth), maximum body length and trophic diversity to examine how dietary specialization has influenced morphological diversification in this rapid radiation. We show that sea snake body shape and size are strongly correlated with the proportion of burrowing prey in the diet. Specialist predators of burrowing eels have convergently evolved a 'microcephalic' morphotype with dramatically reduced forebody relative to hindbody girth and intermediate body length. By comparison, snakes that predominantly feed on burrowing gobies are generally short-bodied and small-headed, but there is no evidence of convergent evolution. The eel specialists also exhibit faster rates of size and shape evolution compared to all other sea snakes, including those that feed on gobies. Our results suggest that trophic specialization to particular burrowing prey (eels) has invoked strong selective pressures that manifest as predictable and rapid morphological changes. Further studies are needed to examine the genetic and developmental mechanisms underlying these dramatic morphological changes and assess their role in sea snake speciation.

Enemy at the gates: Rapid defensive trait diversification in an adaptive radiation of lizards.

PubMed

Broeckhoven, Chris; Diedericks, Genevieve; Hui, Cang; Makhubo, Buyisile G; Mouton, P le Fras N

2016-11-01

Adaptive radiation (AR), the product of rapid diversification of an ancestral species into novel adaptive zones, has become pivotal in our understanding of biodiversity. Although it has widely been accepted that predators may drive the process of AR by creating ecological opportunity (e.g., enemy-free space), the role of predators as selective agents in defensive trait diversification remains controversial. Using phylogenetic comparative methods, we provide evidence for an "early burst" in the diversification of antipredator phenotypes in Cordylinae, a relatively small AR of morphologically diverse southern African lizards. The evolution of body armor appears to have been initially rapid, but slowed down over time, consistent with the ecological niche-filling model. We suggest that the observed "early burst" pattern could be attributed to shifts in vulnerability to different types of predators (i.e., aerial versus terrestrial) associated with thermal habitat partitioning. These results provide empirical evidence supporting the hypothesis that predators or the interaction therewith might be key components of ecological opportunity, although the way in which predators influence morphological diversification requires further study. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Duplicate Abalone Egg Coat Proteins Bind Sperm Lysin Similarly, but Evolve Oppositely, Consistent with Molecular Mimicry at Fertilization

PubMed Central

Aagaard, Jan E.; Springer, Stevan A.; Soelberg, Scott D.; Swanson, Willie J.

2013-01-01

Sperm and egg proteins constitute a remarkable paradigm in evolutionary biology: despite their fundamental role in mediating fertilization (suggesting stasis), some of these molecules are among the most rapidly evolving ones known, and their divergence can lead to reproductive isolation. Because of strong selection to maintain function among interbreeding individuals, interacting fertilization proteins should also exhibit a strong signal of correlated divergence among closely related species. We use evidence of such molecular co-evolution to target biochemical studies of fertilization in North Pacific abalone (Haliotis spp.), a model system of reproductive protein evolution. We test the evolutionary rates (d N/d S) of abalone sperm lysin and two duplicated egg coat proteins (VERL and VEZP14), and find a signal of co-evolution specific to ZP-N, a putative sperm binding motif previously identified by homology modeling. Positively selected residues in VERL and VEZP14 occur on the same face of the structural model, suggesting a common mode of interaction with sperm lysin. We test this computational prediction biochemically, confirming that the ZP-N motif is sufficient to bind lysin and that the affinities of VERL and VEZP14 are comparable. However, we also find that on phylogenetic lineages where lysin and VERL evolve rapidly, VEZP14 evolves slowly, and vice versa. We describe a model of sexual conflict that can recreate this pattern of anti-correlated evolution by assuming that VEZP14 acts as a VERL mimic, reducing the intensity of sexual conflict and slowing the co-evolution of lysin and VERL. PMID:23408913

Flight Planning for the International Space Station-Levitation Observation of Dendrite Evolution in Steel Ternary Alloy Rapid Solidification

NASA Technical Reports Server (NTRS)

Flemings, M. C.; Matson, D. M.; Loser, W.; Hyers, R. W.; Rogers, J. R.; Curreri, Peter A. (Technical Monitor)

2002-01-01

The paper is an overview of the status and science for the LODESTARS (Levitation Observation of Dendrite Evolution in Steel Ternary Alloy Rapid Solidification) research project. The program is aimed at understanding how melt convection influences phase selection and the evolution of rapid solidification microstructures.

Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii

PubMed Central

Ratcliff, William C.; Herron, Matthew D.; Howell, Kathryn; Pentz, Jennifer T.; Rosenzweig, Frank; Travisano, Michael

2013-01-01

The transition to multicellularity enabled the evolution of large, complex organisms, but early steps in this transition remain poorly understood. Here we show that multicellular complexity, including development from a single cell, can evolve rapidly in a unicellular organism that has never had a multicellular ancestor. We subject the alga Chlamydomonas reinhardtii to conditions that favour multicellularity, resulting in the evolution of a multicellular life cycle in which clusters reproduce via motile unicellular propagules. While a single-cell genetic bottleneck during ontogeny is widely regarded as an adaptation to limit among-cell conflict, its appearance very early in this transition suggests that it did not evolve for this purpose. Instead, we find that unicellular propagules are adaptive even in the absence of intercellular conflict, maximizing cluster-level fecundity. These results demonstrate that the unicellular bottleneck, a trait essential for evolving multicellular complexity, can arise rapidly via co-option of the ancestral unicellular form. PMID:24193369

Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly.

PubMed

Aird, Steven D; Aggarwal, Shikha; Villar-Briones, Alejandro; Tin, Mandy Man-Ying; Terada, Kouki; Mikheyev, Alexander S

2015-08-28

While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Using next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05 %). Hybrids produced most proteins found in both parental venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation. Given log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that as a result of natural selection, snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive evolution of venoms may occur most rapidly through changes in expression levels that alter fitness contributions, and thus the strength of selection acting on specific secretome components.

Does rapid evolution matter? Measuring the rate of contemporary evolution and its impacts on ecological dynamics.

PubMed

Ellner, Stephen P; Geber, Monica A; Hairston, Nelson G

2011-06-01

Rapid contemporary evolution due to natural selection is common in the wild, but it remains uncertain whether its effects are an essential component of community and ecosystem structure and function. Previously we showed how to partition change in a population, community or ecosystem property into contributions from environmental and trait change, when trait change is entirely caused by evolution (Hairston et al. 2005). However, when substantial non-heritable trait change occurs (e.g. due to phenotypic plasticity or change in population structure) that approach can mis-estimate both contributions. Here, we demonstrate how to disentangle ecological impacts of evolution vs. non-heritable trait change by combining our previous approach with the Price Equation. This yields a three-way partitioning into effects of evolution, non-heritable phenotypic change and environment. We extend the approach to cases where ecological consequences of trait change are mediated through interspecific interactions. We analyse empirical examples involving fish, birds and zooplankton, finding that the proportional contribution of rapid evolution varies widely (even among different ecological properties affected by the same trait), and that rapid evolution can be important when it acts to oppose and mitigate phenotypic effects of environmental change. Paradoxically, rapid evolution may be most important when it is least evident. © 2011 Blackwell Publishing Ltd/CNRS.

Collaborative Action Research for Middle Grades Improvement

ERIC Educational Resources Information Center

Downes, John M.; Bishop, Penny A.; Swallow, Meredith; Olofson, Mark; Hennessey, Susan

2016-01-01

Technology's rapid evolution applies constant pressure to educational organizations, suggesting a need to continually re-envision schools for the digital age. Yet educators often struggle to understand the growing chasm between students' out-of-school and in-school technology lives. This gap is particularly noticeable during the middle grades…

Rapid evolution of the intersexual genetic correlation for fitness in Drosophila melanogaster.

PubMed

Collet, Julie M; Fuentes, Sara; Hesketh, Jack; Hill, Mark S; Innocenti, Paolo; Morrow, Edward H; Fowler, Kevin; Reuter, Max

2016-04-01

Sexual antagonism (SA) arises when male and female phenotypes are under opposing selection, yet genetically correlated. Until resolved, antagonism limits evolution toward optimal sex-specific phenotypes. Despite its importance for sex-specific adaptation and existing theory, the dynamics of SA resolution are not well understood empirically. Here, we present data from Drosophila melanogaster, compatible with a resolution of SA. We compared two independent replicates of the "LHM " population in which SA had previously been described. Both had been maintained under identical, controlled conditions, and separated for around 200 generations. Although heritabilities of male and female fitness were similar, the intersexual genetic correlation differed significantly, being negative in one replicate (indicating SA) but close to zero in the other. Using population sequencing, we show that phenotypic differences were associated with population divergence in allele frequencies at nonrandom loci across the genome. Large frequency changes were more prevalent in the population without SA and were enriched at loci mapping to genes previously shown to have sexually antagonistic relationships between expression and fitness. Our data suggest that rapid evolution toward SA resolution has occurred in one of the populations and open avenues toward studying the genetics of SA and its resolution. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Reverse Evolution of Armor Plates in the Threespine Stickleback

USGS Publications Warehouse

Kitano, J.; Bolnick, D.I.; Beauchamp, D.A.; Mazur, M.M.; Mori, S.; Nakano, T.; Peichel, C.L.

2008-01-01

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not??only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of "reverse evolution," [9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime. ?? 2008 Elsevier Ltd. All rights reserved.

Origin and Evolution of the Sponge Aggregation Factor Gene Family.

PubMed

Grice, Laura F; Gauthier, Marie E A; Roper, Kathrein E; Fernàndez-Busquets, Xavier; Degnan, Sandie M; Degnan, Bernard M

2017-05-01

Although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. Here, we characterize the Aggregation Factor (AF) gene family, which encodes putative allorecognition factors in the demosponge Amphimedon queenslandica, and trace its evolution across 24 sponge (Porifera) species. The AF locus in Amphimedon is comprised of a cluster of five similar genes that encode Calx-beta and Von Willebrand domains and a newly defined Wreath domain, and are highly polymorphic. Further AF variance appears to be generated through individualistic patterns of RNA editing. The AF gene family varies between poriferans, with protein sequences and domains diagnostic of the AF family being present in Amphimedon and other demosponges, but absent from other sponge classes. Within the demosponges, AFs vary widely with no two species having the same AF repertoire or domain organization. The evolution of AFs suggests that their diversification occurs via high allelism, and the continual and rapid gain, loss and shuffling of domains over evolutionary time. Given the marked differences in metazoan allorecognition genes, we propose the rapid evolution of AFs in sponges provides a model for understanding the extensive diversification of self-nonself recognition systems in the animal kingdom. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Structural defects and variations in the HIV-1 nef gene from rapid, slow and non-progressor children.

PubMed

Casartelli, Nicoletta; Di Matteo, Gigliola; Argentini, Claudio; Cancrini, Caterina; Bernardi, Stefania; Castelli, Guido; Scarlatti, Gabriella; Plebani, Anna; Rossi, Paolo; Doria, Margherita

2003-06-13

Evaluation of sequence evolution as well as structural defects and mutations of the human immunodeficiency virus-type 1 (HIV-1) nef gene in relation to disease progression in infected children. We examined a large number of nef alleles sequentially derived from perinatally HIV-1-infected children with different rates of disease progression: six non-progressors (NPs), four rapid progressors (RPs), and three slow progressors (SPs). Nef alleles (182 total) were isolated from patients' peripheral blood mononuclear cells (PBMCs), sequenced and analysed for their evolutionary pattern, frequency of mutations and occurrence of amino acid variations associated with different stages of disease. The evolution rate of the nef gene apparently correlated with CD4+ decline in all progression groups. Evidence for rapid viral turnover and positive selection for changes were found only in two SPs and two RPs respectively. In NPs, a higher proportion of disrupted sequences and mutations at various functional motifs were observed. Furthermore, NP-derived Nef proteins were often changed at residues localized in the folded core domain at cytotoxic T lymphocytes (CTL) epitopes (E(105), K(106), E(110), Y(132), K(164), and R(200)), while other residues outside the core domain are more often changed in RPs (A(43)) and SPs (N(173) and Y(214)). Our results suggest a link between nef gene functions and the progression rate in HIV-1-infected children. Moreover, non-progressor-associated variations in the core domain of Nef, together with the genetic analysis, suggest that nef gene evolution is shaped by an effective immune system in these patients.

Consequences of Chixculub Impact for the Tectonic and Geodynamic Evolution of the Gulf of Mexico North Carribean Region

NASA Astrophysics Data System (ADS)

Rangin, C.; Crespy, A.; Martinez-Reyes, J.

2013-05-01

The debate for Pacific exotic origin versus in situ inter American plate Atlantic origin of the Caribbean plate is active in the scientific community since decades. Independently of the origin of this plate, its fast motion towards the east at a present rate of 2cm/yr is accepted to have been initiated during the early-most Cenozoic. The Paleocene is a key period in the global evolution of Central America mainly marked also by the Chicxulub multiring meteor impact in Yucatan. We question here the genetic relationship between this impact event and the incipient tectonic escape of the Caribbean plate. The mostly recent published models suggest this impact has affected the whole crust down to the Moho, the upper mantle being rapidly and considerably uplifted. The crust was then fragmented 600km at least from the point of impact, and large circular depressions were rapidly filled by clastic sediments from Cantarell to Western Cuba via Chiapas and Belize. North of the impact, the whole Gulf of Mexico was affected by mass gravity sliding, initiated also during the Paleocene in Texas, remaining active in this basin up to present time. South of the impact, in the Caribbean plate, the Yucatan basin was rapidly opened, indicating a fast escape of the crustal material towards the unique free boundary, the paleo-Antilles subduction zone. Shear waves velocity data below the Caribbean plate suggest this crustal tectonic escape was enhanced by the fast eastward flowing mantle supporting a fragmented and stretched crust. The proposed model suggests Chicxulub impact (but also the hypothetic Beata impact) have fragmented brittle crust, then easily drifted towards the east. This could explain the Paleogene evolution of the Caribbean plate largely stretched during its early evolution. Geologically, this evolution could explain the absence of evident Paleogene oblique subduction along the Caribbean plate northern and southern margins, marked only by Mid Cretaceous dragged volcanic complexes, but also the relatively recent motion along the Cayman Fault zone (Miocene instead of Eocene). These results are part of a cooperative research-industry programm conducted by CEREGE/EGERIE, Aix-en-Provence and GeoAzur, Nice, with Frontier Basin study group TOTAL S.A., Paris.

Experimental evolution reveals genome-wide spectrum and dynamics of mutations in the rice blast fungus, Magnaporthe oryzae.

PubMed

Jeon, Junhyun; Choi, Jaeyoung; Lee, Gir-Won; Dean, Ralph A; Lee, Yong-Hwan

2013-01-01

Knowledge on mutation processes is central to interpreting genetic analysis data as well as understanding the underlying nature of almost all evolutionary phenomena. However, studies on genome-wide mutational spectrum and dynamics in fungal pathogens are scarce, hindering our understanding of their evolution and biology. Here, we explored changes in the phenotypes and genome sequences of the rice blast fungus Magnaporthe oryzae during the forced in vitro evolution by weekly transfer of cultures on artificial media. Through combination of experimental evolution with high throughput sequencing technology, we found that mutations accumulate rapidly prior to visible phenotypic changes and that both genetic drift and selection seem to contribute to shaping mutational landscape, suggesting the buffering capacity of fungal genome against mutations. Inference of mutational effects on phenotypes through the use of T-DNA insertion mutants suggested that at least some of the DNA sequence mutations are likely associated with the observed phenotypic changes. Furthermore, our data suggest oxidative damages and UV as major sources of mutation during subcultures. Taken together, our work revealed important properties of original source of variation in the genome of the rice blast fungus. We believe that these results provide not only insights into stability of pathogenicity and genome evolution in plant pathogenic fungi but also a model in which evolution of fungal pathogens in natura can be comparatively investigated.

Origin and Evolution of the Sponge Aggregation Factor Gene Family

PubMed Central

Grice, Laura F.; Gauthier, Marie E.A.; Roper, Kathrein E.; Fernàndez-Busquets, Xavier; Degnan, Sandie M.

2017-01-01

Although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. Here, we characterize the Aggregation Factor (AF) gene family, which encodes putative allorecognition factors in the demosponge Amphimedon queenslandica, and trace its evolution across 24 sponge (Porifera) species. The AF locus in Amphimedon is comprised of a cluster of five similar genes that encode Calx-beta and Von Willebrand domains and a newly defined Wreath domain, and are highly polymorphic. Further AF variance appears to be generated through individualistic patterns of RNA editing. The AF gene family varies between poriferans, with protein sequences and domains diagnostic of the AF family being present in Amphimedon and other demosponges, but absent from other sponge classes. Within the demosponges, AFs vary widely with no two species having the same AF repertoire or domain organization. The evolution of AFs suggests that their diversification occurs via high allelism, and the continual and rapid gain, loss and shuffling of domains over evolutionary time. Given the marked differences in metazoan allorecognition genes, we propose the rapid evolution of AFs in sponges provides a model for understanding the extensive diversification of self–nonself recognition systems in the animal kingdom. PMID:28104746

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

PubMed Central

Hou, Beiwei; Luo, Jing; Zhang, Yusi; Niu, Zhitao; Xue, Qingyun; Ding, Xiaoyu

2017-01-01

The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species’ diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange. PMID:28262789

Evosystem Services: Rapid Evolution and the Provision of Ecosystem Services.

PubMed

Rudman, Seth M; Kreitzman, Maayan; Chan, Kai M A; Schluter, Dolph

2017-06-01

Evolution is recognized as the source of all organisms, and hence many ecosystem services. However, the role that contemporary evolution might play in maintaining and enhancing specific ecosystem services has largely been overlooked. Recent advances at the interface of ecology and evolution have demonstrated how contemporary evolution can shape ecological communities and ecosystem functions. We propose a definition and quantitative criteria to study how rapid evolution affects ecosystem services (here termed contemporary evosystem services) and present plausible scenarios where such services might exist. We advocate for the direct measurement of contemporary evosystem services to improve understanding of how changing environments will alter resource availability and human well-being, and highlight the potential utility of managing rapid evolution for future ecosystem services. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage

PubMed Central

Benson, Roger B. J.; Campione, Nicolás E.; Carrano, Matthew T.; Mannion, Philip D.; Sullivan, Corwin; Upchurch, Paul; Evans, David C.

2014-01-01

Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation, representing an ecologically diverse group that dominated terrestrial ecosystems for 170 million years. Furthermore, with 10,000 species, extant dinosaurs (birds) are the most speciose living tetrapod clade. We assembled composite trees of 614–622 Mesozoic dinosaurs/birds, and a comprehensive body mass dataset using the scaling relationship of limb bone robustness. Maximum-likelihood modelling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts among size classes in early (Triassic) dinosaurs. This indicates an early burst niche-filling pattern and contrasts with previous studies that favoured gradualistic rates. Subsequently, rates declined in most lineages, which rarely exploited new ecological niches. However, feathered maniraptoran dinosaurs (including Mesozoic birds) sustained rapid evolution from at least the Middle Jurassic, suggesting that these taxa evaded the effects of niche saturation. This indicates that a long evolutionary history of continuing ecological innovation paved the way for a second great radiation of dinosaurs, in birds. We therefore demonstrate links between the predominantly extinct deep time adaptive radiation of non-avian dinosaurs and the phenomenal diversification of birds, via continuing rapid rates of evolution along the phylogenetic stem lineage. This raises the possibility that the uneven distribution of biodiversity results not just from large-scale extrapolation of the process of adaptive radiation in a few extant clades, but also from the maintenance of evolvability on vast time scales across the history of life, in key lineages. PMID:24802911

Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage.

PubMed

Benson, Roger B J; Campione, Nicolás E; Carrano, Matthew T; Mannion, Philip D; Sullivan, Corwin; Upchurch, Paul; Evans, David C

2014-05-01

Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation, representing an ecologically diverse group that dominated terrestrial ecosystems for 170 million years. Furthermore, with 10,000 species, extant dinosaurs (birds) are the most speciose living tetrapod clade. We assembled composite trees of 614-622 Mesozoic dinosaurs/birds, and a comprehensive body mass dataset using the scaling relationship of limb bone robustness. Maximum-likelihood modelling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts among size classes in early (Triassic) dinosaurs. This indicates an early burst niche-filling pattern and contrasts with previous studies that favoured gradualistic rates. Subsequently, rates declined in most lineages, which rarely exploited new ecological niches. However, feathered maniraptoran dinosaurs (including Mesozoic birds) sustained rapid evolution from at least the Middle Jurassic, suggesting that these taxa evaded the effects of niche saturation. This indicates that a long evolutionary history of continuing ecological innovation paved the way for a second great radiation of dinosaurs, in birds. We therefore demonstrate links between the predominantly extinct deep time adaptive radiation of non-avian dinosaurs and the phenomenal diversification of birds, via continuing rapid rates of evolution along the phylogenetic stem lineage. This raises the possibility that the uneven distribution of biodiversity results not just from large-scale extrapolation of the process of adaptive radiation in a few extant clades, but also from the maintenance of evolvability on vast time scales across the history of life, in key lineages.

Probing the Boundaries of Orthology: The Unanticipated Rapid Evolution of Drosophila centrosomin

PubMed Central

Eisman, Robert C.; Kaufman, Thomas C.

2013-01-01

The rapid evolution of essential developmental genes and their protein products is both intriguing and problematic. The rapid evolution of gene products with simple protein folds and a lack of well-characterized functional domains typically result in a low discovery rate of orthologous genes. Additionally, in the absence of orthologs it is difficult to study the processes and mechanisms underlying rapid evolution. In this study, we have investigated the rapid evolution of centrosomin (cnn), an essential gene encoding centrosomal protein isoforms required during syncytial development in Drosophila melanogaster. Until recently the rapid divergence of cnn made identification of orthologs difficult and questionable because Cnn violates many of the assumptions underlying models for protein evolution. To overcome these limitations, we have identified a group of insect orthologs and present conserved features likely to be required for the functions attributed to cnn in D. melanogaster. We also show that the rapid divergence of Cnn isoforms is apparently due to frequent coding sequence indels and an accelerated rate of intronic additions and eliminations. These changes appear to be buffered by multi-exon and multi-reading frame maximum potential ORFs, simple protein folds, and the splicing machinery. These buffering features also occur in other genes in Drosophila and may help prevent potentially deleterious mutations due to indels in genes with large coding exons and exon-dense regions separated by small introns. This work promises to be useful for future investigations of cnn and potentially other rapidly evolving genes and proteins. PMID:23749319

Duplicated genes evolve independently in allopolyploid cotton.

Treesearch

Richard C. Cronn; Randall L. Small; Jonathan F. Wendel

1999-01-01

Of the many processes that generate gene duplications, polyploidy is unique in that entire genomes are duplicated. This process has been important in the evolution of many eukaryotic groups, and it occurs with high frequency in plants. Recent evidence suggests that polyploidization may be accompanied by rapid genomic changes, but the evolutionary fate of discrete loci...

Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods.

PubMed

Chang, Dan; Duda, Thomas F

2014-06-05

Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components ('conotoxins'), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species' 'venom gene space'. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization. Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci ('under-dispersed' expression of available genes) while others express sets of more disparate genes ('over-dispersed' expression). In addition, expressed genes show higher dN/dS values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication. Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species.

Biomechanical consequences of rapid evolution in the polar bear lineage.

PubMed

Slater, Graham J; Figueirido, Borja; Louis, Leeann; Yang, Paul; Van Valkenburgh, Blaire

2010-11-05

The polar bear is the only living ursid with a fully carnivorous diet. Despite a number of well-documented craniodental adaptations for a diet of seal flesh and blubber, molecular and paleontological data indicate that this morphologically distinct species evolved less than a million years ago from the omnivorous brown bear. To better understand the evolution of this dietary specialization, we used phylogenetic tests to estimate the rate of morphological specialization in polar bears. We then used finite element analysis (FEA) to compare the limits of feeding performance in the polar bear skull to that of the phylogenetically and geographically close brown bear. Results indicate that extremely rapid evolution of semi-aquatic adaptations and dietary specialization in the polar bear lineage produced a cranial morphology that is weaker than that of brown bears and less suited to processing tough omnivorous or herbivorous diets. Our results suggest that continuation of current climate trends could affect polar bears by not only eliminating their primary food source, but also through competition with northward advancing, generalized brown populations for resources that they are ill-equipped to utilize.

Electromagnetic induction heating for single crystal graphene growth: morphology control by rapid heating and quenching

NASA Astrophysics Data System (ADS)

Wu, Chaoxing; Li, Fushan; Chen, Wei; Veeramalai, Chandrasekar Perumal; Ooi, Poh Choon; Guo, Tailiang

2015-03-01

The direct observation of single crystal graphene growth and its shape evolution is of fundamental importance to the understanding of graphene growth physicochemical mechanisms and the achievement of wafer-scale single crystalline graphene. Here we demonstrate the controlled formation of single crystal graphene with varying shapes, and directly observe the shape evolution of single crystal graphene by developing a localized-heating and rapid-quenching chemical vapor deposition (CVD) system based on electromagnetic induction heating. Importantly, rational control of circular, hexagonal, and dendritic single crystalline graphene domains can be readily obtained for the first time by changing the growth condition. Systematic studies suggest that the graphene nucleation only occurs during the initial stage, while the domain density is independent of the growth temperatures due to the surface-limiting effect. In addition, the direct observation of graphene domain shape evolution is employed for the identification of competing growth mechanisms including diffusion-limited, attachment-limited, and detachment-limited processes. Our study not only provides a novel method for morphology-controlled graphene synthesis, but also offers fundamental insights into the kinetics of single crystal graphene growth.

Recent speciation in the Indo-West Pacific: rapid evolution of gamete recognition and sperm morphology in cryptic species of sea urchin.

PubMed Central

Landry, C; Geyer, L B; Arakaki, Y; Uehara, T; Palumbi, Stephen R

2003-01-01

The rich species diversity of the marine Indo-West Pacific (IWP) has been explained largely on the basis of historical observation of large-scale diversity gradients. Careful study of divergence among closely related species can reveal important new information about the pace and mechanisms of their formation, and can illuminate the genesis of biogeographic patterns. Young species inhabiting the IWP include urchins of the genus Echinometra, which diverged over the past 1-5 Myr. Here, we report the most recent divergence of two cryptic species of Echinometra inhabiting this region. Mitochondrial cytochrome oxidase 1 (CO1) sequence data show that in Echinometra oblonga, species-level divergence in sperm morphology, gamete recognition proteins and gamete compatibility arose between central and western Pacific populations in the past 250 000 years. Divergence in sperm attachment proteins suggests rapid evolution of the fertilization system. Divergence of sperm morphology may be a common feature of free-spawning animals, and offers opportunities to simultaneously understand genetic divergence, changes in protein expression patterns and morphological evolution in traits directly related to reproductive isolation. PMID:12964987

Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest

Treesearch

Ryan R. Bracewell; Barbara J. Bentz; Brian T. Sullivan; Jeffrey M. Good

2017-01-01

Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine...

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

PubMed Central

Reinhardt, Josephine A.; Wanjiru, Betty M.; Brant, Alicia T.; Saelao, Perot; Begun, David J.; Jones, Corbin D.

2013-01-01

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important. PMID:24146629

The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution.

PubMed

Reznick, D N; Ghalambor, C K

2001-01-01

Under what conditions might organisms be capable of rapid adaptive evolution? We reviewed published studies documenting contemporary adaptations in natural populations and looked for general patterns in the population ecological causes. We found that studies of contemporary adaptation fall into two general settings: (1) colonization of new environments that established newly adapted populations, and (2) local adaptations within the context of a heterogeneous environments and metapopulation structure. Local ecological processes associated with colonizations and introductions included exposure to: (1) a novel host or food resource; (2) a new biophysical environment; (3) a new predator community; and (4) a new coexisting competitor. The new environments that were colonized often had depauperate communities, sometimes because of anthropogenic disturbance. Local adaptation in heterogeneous environments was also often associated with recent anthropogenic changes, such as insecticide and herbicide resistance, or industrial melanism. A common feature of many examples is the combination of directional selection with at least a short-term opportunity for population growth. We suggest that such opportunities for population growth may be a key factor that promotes rapid evolution, since directional selection might otherwise be expected to cause population decline and create the potential for local extinction, which is an ever-present alternative to local adaptation. We also address the large discrepancy between the rate of evolution observed in contemporary studies and the apparent rate of evolution seen in the fossil record.

Similar traits, different genes? Examining convergent evolution in related weedy rice populations.

PubMed

Thurber, Carrie S; Jia, Melissa H; Jia, Yulin; Caicedo, Ana L

2013-02-01

Convergent phenotypic evolution may or may not be associated with convergent genotypic evolution. Agricultural weeds have repeatedly been selected for weed-adaptive traits such as rapid growth, increased seed dispersal and dormancy, thus providing an ideal system for the study of convergent evolution. Here, we identify QTL underlying weedy traits and compare their genetic architecture to assess the potential for convergent genetic evolution in two distinct populations of weedy rice. F(2) offspring from crosses between an indica cultivar and two individuals from genetically differentiated U.S. weedy rice populations were used to map QTL for four quantitative (heading date, seed shattering, plant height and growth rate) and two qualitative traits. We identified QTL on nine of the twelve rice chromosomes, yet most QTL locations do not overlap between the two populations. Shared QTL among weed groups were only seen for heading date, a trait for which weedy groups have diverged from their cultivated ancestors and from each other. Sharing of some QTL with wild rice also suggests a possible role in weed evolution for genes under selection during domestication. The lack of overlapping QTL for the remaining traits suggests that, despite a close evolutionary relationship, weedy rice groups have adapted to the same agricultural environment through different genetic mechanisms. © 2012 Blackwell Publishing Ltd.

Big bang in the evolution of extant malaria parasites.

PubMed

Hayakawa, Toshiyuki; Culleton, Richard; Otani, Hiroto; Horii, Toshihiro; Tanabe, Kazuyuki

2008-10-01

Malaria parasites (genus Plasmodium) infect all classes of terrestrial vertebrates and display host specificity in their infections. It is therefore assumed that malaria parasites coevolved intimately with their hosts. Here, we propose a novel scenario of malaria parasite-host coevolution. A phylogenetic tree constructed using the malaria parasite mitochondrial genome reveals that the extant primate, rodent, bird, and reptile parasite lineages rapidly diverged from a common ancestor during an evolutionary short time period. This rapid diversification occurred long after the establishment of the primate, rodent, bird, and reptile host lineages, which implies that host-switch events contributed to the rapid diversification of extant malaria parasite lineages. Interestingly, the rapid diversification coincides with the radiation of the mammalian genera, suggesting that adaptive radiation to new mammalian hosts triggered the rapid diversification of extant malaria parasite lineages.

Evolution in leaps: The punctuated accumulation and loss of cultural innovations

PubMed Central

Kolodny, Oren; Creanza, Nicole; Feldman, Marcus W.

2015-01-01

Archaeological accounts of cultural change reveal a fundamental conflict: Some suggest that change is gradual, accelerating over time, whereas others indicate that it is punctuated, with long periods of stasis interspersed by sudden gains or losses of multiple traits. Existing models of cultural evolution, inspired by models of genetic evolution, lend support to the former and do not generate trajectories that include large-scale punctuated change. We propose a simple model that can give rise to both exponential and punctuated patterns of gain and loss of cultural traits. In it, cultural innovation comprises several realistic interdependent processes that occur at different rates. The model also takes into account two properties intrinsic to cultural evolution: the differential distribution of traits among social groups and the impact of environmental change. In our model, a population may be subdivided into groups with different cultural repertoires leading to increased susceptibility to cultural loss, whereas environmental change may lead to rapid loss of traits that are not useful in a new environment. Taken together, our results suggest the usefulness of a concept of an effective cultural population size. PMID:26598675

Evolution in leaps: The punctuated accumulation and loss of cultural innovations.

PubMed

Kolodny, Oren; Creanza, Nicole; Feldman, Marcus W

2015-12-08

Archaeological accounts of cultural change reveal a fundamental conflict: Some suggest that change is gradual, accelerating over time, whereas others indicate that it is punctuated, with long periods of stasis interspersed by sudden gains or losses of multiple traits. Existing models of cultural evolution, inspired by models of genetic evolution, lend support to the former and do not generate trajectories that include large-scale punctuated change. We propose a simple model that can give rise to both exponential and punctuated patterns of gain and loss of cultural traits. In it, cultural innovation comprises several realistic interdependent processes that occur at different rates. The model also takes into account two properties intrinsic to cultural evolution: the differential distribution of traits among social groups and the impact of environmental change. In our model, a population may be subdivided into groups with different cultural repertoires leading to increased susceptibility to cultural loss, whereas environmental change may lead to rapid loss of traits that are not useful in a new environment. Taken together, our results suggest the usefulness of a concept of an effective cultural population size.

Extant-only comparative methods fail to recover the disparity preserved in the bird fossil record.

PubMed

Mitchell, Jonathan S

2015-09-01

Most extant species are in clades with poor fossil records, and recent studies of comparative methods show they have low power to infer even highly simplified models of trait evolution without fossil data. Birds are a well-studied radiation, yet their early evolutionary patterns are still contentious. The fossil record suggests that birds underwent a rapid ecological radiation after the end-Cretaceous mass extinction, and several smaller, subsequent radiations. This hypothesized series of repeated radiations from fossil data is difficult to test using extant data alone. By uniting morphological and phylogenetic data on 604 extant genera of birds with morphological data on 58 species of extinct birds from 50 million years ago, the "halfway point" of avian evolution, I have been able to test how well extant-only methods predict the diversity of fossil forms. All extant-only methods underestimate the disparity, although the ratio of within- to between-clade disparity does suggest high early rates. The failure of standard models to predict high early disparity suggests that recent radiations are obscuring deep time patterns in the evolution of birds. Metrics from different models can be used in conjunction to provide more valuable insights than simply finding the model with the highest relative fit. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota.

PubMed

Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A; McHardy, Alice C; Embley, T Martin; Prosser, James I; Macqueen, Daniel J

2015-07-28

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400-700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum.

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

PubMed Central

Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A.; McHardy, Alice C.; Embley, T. Martin; Prosser, James I.; Macqueen, Daniel J.

2015-01-01

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400–700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum. PMID:26170282

On meme--gene coevolution.

PubMed

Bull, L; Holland, O; Blackmore, S

2000-01-01

In this article we examine the effects of the emergence of a new replicator, memes, on the evolution of a pre-existing replicator, genes. Using a version of the NKCS model we examine the effects of increasing the rate of meme evolution in relation to the rate of gene evolution, for various degrees of interdependence between the two replicators. That is, the effects of memes' (suggested) more rapid rate of evolution in comparison to that of genes is investigated using a tunable model of coevolution. It is found that, for almost any degree of interdependence between the two replicators, as the rate of meme evolution increases, a phase transition-like dynamic occurs under which memes have a significantly detrimental effect on the evolution of genes, quickly resulting in the cessation of effective gene evolution. Conversely, the memes experience a sharp increase in benefit from increasing their rate of evolution. We then examine the effects of enabling genes to reduce the percentage of gene-detrimental evolutionary steps taken by memes. Here a critical region emerges as the comparative rate of meme evolution increases, such that if genes cannot effectively select memes a high percentage of the time, they suffer from meme evolution as if they had almost no selective capability.

We really need to talk: adapting FDA processes to rapid change.

PubMed

Lykken, Sara

2013-01-01

The rapidly evolving realm of modern commerce strains traditional regulatory paradigms. This paper traces the historical evolution of FDA crisis-response regulation and provides examples of ways in which the definitions and procedures resulting from that past continue to be challenged by new products as market entrants, some in good faith and others not, take actions that create disconnects between actual product and marketing controls and those that consumers might expect. The paper then explores some of the techniques used by other federal agencies that have faced similar challenges in environments characterized by rapid innovation, and draws from this analysis suggestions for improvement of the FDA's warning letter system.

A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae

PubMed Central

2010-01-01

Background The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. Results We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). Conclusions The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution. PMID:20444289

The evolution of ecological tolerance in prokaryotes

NASA Technical Reports Server (NTRS)

Knoll, A. H.; Bauld, J.

1989-01-01

The ecological ranges of Archaeobacteria and Eubacteria are constrained by a requirement for liquid water and the physico-chemical stability limits of biomolecules, but within this broad envelope, prokaryotes have evolved adaptations that permit them to tolerate a remarkable spectrum of habitats. Laboratory experiments indicate that prokaryotes can adapt rapidly to novel environmental conditions, yet geological studies suggest early diversification and long-term stasis within the prokaryotic kingdoms. These apparently contradictory perspectives can be reconciled by understanding that, in general, rates and patterns of prokaryotic evolution reflect the developmental history of the Earth's surface environments. Our understanding of modern microbial ecology provides a lens through which our accumulating knowledge of physiology, molecular phylogeny and the Earth's history can be integrated and focussed on the phenomenon of prokaryotic evolution.

Secular Evolution in Barred Galaxies: Observations

NASA Astrophysics Data System (ADS)

Merrifield, M.

2002-12-01

This paper describes a framework for studying galaxy morphology, particularly bar strength, in a quantitative manner, and presents applications of this approach that reveal observational evidence for secular evolution in bar morphology. The distribution of bar strength in galaxies is quite strongly bimodal, suggesting that barred and unbarred systems are distinct entities, and that any evolution between these two states must occur on a relatively rapid timescale. Bars' strengths appear to be correlated with their pattern speeds, implying that these structures weaken as they start to slow, and disappear entirely before the bars have slowed significantly. There is also tantalizing evidence that bars are rare beyond a redshift of z ~ 0.7, indicating that galaxies have only recently evolved to a point where bars can readily form.

Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection

PubMed Central

Zhang, Jianzhi; Dyer, Kimberly D.; Rosenberg, Helene F.

2000-01-01

The mammalian RNase A superfamily comprises a diverse array of ribonucleolytic proteins that have a variety of biochemical activities and physiological functions. Two rapidly evolving RNases of higher primates are of particular interest as they are major secretory proteins of eosinophilic leukocytes and have been found to possess anti-pathogen activities in vitro. To understand how these RNases acquired this function during evolution and to develop animal models for the study of their functions in vivo, it is necessary to investigate these genes in many species. Here, we report the sequences of 38 functional genes and 23 pseudogenes of the eosinophil-associated RNase (EAR) family from 5 rodent species. Our phylogenetic analysis of these genes showed a clear pattern of evolution by a rapid birth-and-death process and gene sorting, a process characterized by rapid gene duplication and deactivation occurring differentially among lineages. This process ultimately generates distinct or only partially overlapping inventories of the genes, even in closely related species. Positive Darwinian selection also contributed to the diversification of these EAR genes. The striking similarity between the evolutionary patterns of the EAR genes and those of the major histocompatibility complex, immunoglobulin, and T cell receptor genes stands in strong support of the hypothesis that host-defense and generation of diversity are among the primary physiological function of the rodent EARs. The discovery of a large number of divergent EARs suggests the intriguing possibility that these proteins have been specifically tailored to fight against distinct rodent pathogens. PMID:10758160

High-temperature morphological evolution of lithographically introduced cavities in silicon carbide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Narushima, Takayuki; Glaeser, Andreas M.

2000-12-01

Internal cavities of controlled geometry and crystallography were introduced in 6H silicon carbide single crystals by combining lithographic methods, ion beam etching, and solid-state diffusion bonding. The morphological evolution of these internal cavities (negative crystals) in response to anneals of up to 128 h duration at 1900 degrees C was examined using optical microscopy. Surface energy anisotropy and faceting have a strong influence on both the geometric and kinetic characteristics of evolution. Decomposition of 12{bar 1}0 cavity edges into 101{bar 0} facets was observed after 16 h anneals, indicating that 12{bar 1}0 faces are not components of the Wulff shape.more » The shape evolution kinetics of penny-shaped cavities were also investigated. Experimentally observed evolution rates decreased much more rapidly with those predicted by a model in which surface diffusion is assumed to be rate-limiting. This suggests that the development of facets, and the associated loss of ledges and terraces during the initial stages of evolution results in an evolution process limited by the nucleation rate of attachment/detachment sites (ledges) on the facets.« less

Tectonic escape of the Caribbean plate since the Paleocene: a consequence of the Chicxulub meteor impact?

NASA Astrophysics Data System (ADS)

Rangin, C.; Martinez-Reyes, J.; Crespy, A.; Zitter, T. A. C.

2012-04-01

The debate for Pacific exotic origin versus in situ inter American plate Atlantic origin of the Caribbean plate is active in the scientific community since decades. Independently of the origin of this plate, its fast motion towards the east at a present rate of 2cm/yr is accepted to have been initiated during the early-most Cenozoic. The Paleocene is a key period in the global evolution of Central America mainly marked also by the Chicxulub multiring meteor impact in Yucatan. We question here the genetic relationship between this impact event and the incipient tectonic escape of the Caribbean plate. The mostly recent published models suggest this impact has affected the whole crust down to the Moho, the upper mantle being rapidly and considerably uplifted. The crust was then fragmented 600km at least from the point of impact, and large circular depressions were rapidly filled by clastic sediments from Cantarell to Western Cuba via Chiapas and Belize. North of the impact, the whole Gulf of Mexico was affected by mass gravity sliding, initiated also during the Paleocene in Texas, remaining active in this basin up to present time. South of the impact, in the Caribbean plate, the Yucatan basin was rapidly opened, indicating a fast escape of the crustal material towards the unique free boundary, the paleo-Antilles subduction zone. Shear waves velocity data below the Caribbean plate suggest this crustal tectonic escape was enhanced by the fast eastward flowing mantle supporting a fragmented and stretched crust. The proposed model suggests Chicxulub impact (but also the hypothetic Beata impact) have fragmented brittle crust, then easily drifted towards the east. This could explain the Paleogene evolution of the Caribbean plate largely stretched during its early evolution. Geologically, this evolution could explain the absence of evident Paleogene oblique subduction along the Caribbean plate northern and southern margins, marked only by Mid Cretaceous dragged volcanic complexes, but also the relatively recent motion along the Cayman Fault zone (Miocene instead of Eocene). These results are part of a cooperative research-industry programm conducted by CEREGE/EGERIE, Aix-en-Provence and GeoAzur, Nice, with Frontier Basin study group, TOTAL S.A., Paris.

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

PubMed

Colautti, Robert I; Lau, Jennifer A

2015-05-01

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

Recycling of wood and paper products in the United States

Treesearch

Peter J. Ince

1996-01-01

This report describes the current status of wood and paper recycling in the United States and predicts the production and market consequences of increased recycling. The results suggest that the rate of paper recycling will rapidly rise in the 1990s, mainly as a result of the competitive evolution of fiber markets and papermaking technologies. The consumption and...

Evolution of Cost-Free Resistance under Fluctuating Drug Selection in Pseudomonas aeruginosa

PubMed Central

McCloskey, Nicholas; Hinz, Aaron J.; Dettman, Jeremy; Kassen, Rees

2017-01-01

ABSTRACT Antibiotic resistance evolves rapidly in response to drug selection, but it can also persist at appreciable levels even after the removal of the antibiotic. This suggests that many resistant strains can both be resistant and have high fitness in the absence of antibiotics. To explore the conditions under which high-fitness, resistant strains evolve and the genetic changes responsible, we used a combination of experimental evolution and whole-genome sequencing to track the acquisition of ciprofloxacin resistance in the opportunistic pathogen Pseudomonas aeruginosa under conditions of constant and fluctuating antibiotic delivery patterns. We found that high-fitness, resistant strains evolved readily under fluctuating but not constant antibiotic conditions and that their evolution was underlain by a trade-off between resistance and fitness. Whole-genome sequencing of evolved isolates revealed that resistance was gained through mutations in known resistance genes and that second-site mutations generally compensated for costs associated with resistance in the fluctuating treatment, leading to the evolution of cost-free resistance. Our results suggest that current therapies involving intermittent administration of antibiotics are contributing to the maintenance of antibiotic resistance at high levels in clinical settings. IMPORTANCE Antibiotic resistance is a global problem that greatly impacts human health. How resistance persists, even in the absence of antibiotic treatment, is thus a public health problem of utmost importance. In this study, we explored the antibiotic treatment conditions under which cost-free resistance arises, using experimental evolution of the bacterium Pseudomonas aeruginosa and the quinolone antibiotic ciprofloxacin. We found that intermittent antibiotic treatment led to the evolution of cost-free resistance and demonstrate that compensatory evolution is the mechanism responsible for cost-free resistance. Our results suggest that discontinuous administration of antibiotic may be contributing to the high levels of antibiotic resistance currently found worldwide. PMID:28744479

Evolution of dispersal and life history interact to drive accelerating spread of an invasive species.

PubMed

Perkins, T Alex; Phillips, Benjamin L; Baskett, Marissa L; Hastings, Alan

2013-08-01

Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life-history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life-history and dispersal evolution during range shift. In roughly equal parts, life-history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion. © 2013 John Wiley & Sons Ltd/CNRS.

Rapid Evolution of Beta-Keratin Genes Contribute to Phenotypic Differences That Distinguish Turtles and Birds from Other Reptiles

PubMed Central

Li, Yang I.; Kong, Lesheng; Ponting, Chris P.; Haerty, Wilfried

2013-01-01

Sequencing of vertebrate genomes permits changes in distinct protein families, including gene gains and losses, to be ascribed to lineage-specific phenotypes. A prominent example of this is the large-scale duplication of beta-keratin genes in the ancestors of birds, which was crucial to the subsequent evolution of their beaks, claws, and feathers. Evidence suggests that the shell of Pseudomys nelsoni contains at least 16 beta-keratins proteins, but it is unknown whether this is a complete set and whether their corresponding genes are orthologous to avian beak, claw, or feather beta-keratin genes. To address these issues and to better understand the evolution of the turtle shell at a molecular level, we surveyed the diversity of beta-keratin genes from the genome assemblies of three turtles, Chrysemys picta, Pelodiscus sinensis, and Chelonia mydas, which together represent over 160 Myr of chelonian evolution. For these three turtles, we found 200 beta-keratins, which indicate that, as for birds, a large expansion of beta-keratin genes in turtles occurred concomitantly with the evolution of a unique phenotype, namely, their plastron and carapace. Phylogenetic reconstruction of beta-keratin gene evolution suggests that separate waves of gene duplication within a single genomic location gave rise to scales, claws, and feathers in birds, and independently the scutes of the shell in turtles. PMID:23576313

How sexual selection can drive the evolution of costly sperm ornamentation

NASA Astrophysics Data System (ADS)

Lüpold, Stefan; Manier, Mollie K.; Puniamoorthy, Nalini; Schoff, Christopher; Starmer, William T.; Luepold, Shannon H. Buckley; Belote, John M.; Pitnick, Scott

2016-05-01

Post-copulatory sexual selection (PSS), fuelled by female promiscuity, is credited with the rapid evolution of sperm quality traits across diverse taxa. Yet, our understanding of the adaptive significance of sperm ornaments and the cryptic female preferences driving their evolution is extremely limited. Here we review the evolutionary allometry of exaggerated sexual traits (for example, antlers, horns, tail feathers, mandibles and dewlaps), show that the giant sperm of some Drosophila species are possibly the most extreme ornaments in all of nature and demonstrate how their existence challenges theories explaining the intensity of sexual selection, mating-system evolution and the fundamental nature of sex differences. We also combine quantitative genetic analyses of interacting sex-specific traits in D. melanogaster with comparative analyses of the condition dependence of male and female reproductive potential across species with varying ornament size to reveal complex dynamics that may underlie sperm-length evolution. Our results suggest that producing few gigantic sperm evolved by (1) Fisherian runaway selection mediated by genetic correlations between sperm length, the female preference for long sperm and female mating frequency, and (2) longer sperm increasing the indirect benefits to females. Our results also suggest that the developmental integration of sperm quality and quantity renders post-copulatory sexual selection on ejaculates unlikely to treat male-male competition and female choice as discrete processes.

Rapid Evolution of Sex Pheromone-Producing Enzyme Expression in Drosophila

PubMed Central

Williams, Thomas M.; Carroll, Sean B.

2009-01-01

A wide range of organisms use sex pheromones to communicate with each other and to identify appropriate mating partners. While the evolution of chemical communication has been suggested to cause sexual isolation and speciation, the mechanisms that govern evolutionary transitions in sex pheromone production are poorly understood. Here, we decipher the molecular mechanisms underlying the rapid evolution in the expression of a gene involved in sex pheromone production in Drosophilid flies. Long-chain cuticular hydrocarbons (e.g., dienes) are produced female-specifically, notably via the activity of the desaturase DESAT-F, and are potent pheromones for male courtship behavior in Drosophila melanogaster. We show that across the genus Drosophila, the expression of this enzyme is correlated with long-chain diene production and has undergone an extraordinary number of evolutionary transitions, including six independent gene inactivations, three losses of expression without gene loss, and two transitions in sex-specificity. Furthermore, we show that evolutionary transitions from monomorphism to dimorphism (and its reversion) in desatF expression involved the gain (and the inactivation) of a binding-site for the sex-determination transcription factor, DOUBLESEX. In addition, we documented a surprising example of the gain of particular cis-regulatory motifs of the desatF locus via a set of small deletions. Together, our results suggest that frequent changes in the expression of pheromone-producing enzymes underlie evolutionary transitions in chemical communication, and reflect changing regimes of sexual selection, which may have contributed to speciation among Drosophila. PMID:19652700

Sexual selection and maintenance of sex: evidence from comparisons of rates of genomic accumulation of mutations and divergence of sex-related genes in sexual and hermaphroditic species of Caenorhabditis.

PubMed

Artieri, Carlo G; Haerty, Wilfried; Gupta, Bhagwati P; Singh, Rama S

2008-05-01

Several hypotheses have been proposed to explain the persistence of dioecy despite the reproductive advantages conferred to hermaphrodites, including greater efficiency at purging deleterious mutations in the former. Dioecy can benefit from both mutation purging and accelerated evolution by bringing together beneficial mutations in the same individual via recombination and shuffling of genotypes. In addition, mathematical treatment has shown that sexual selection is also capable of mitigating the cost of maintaining separate sexes by increasing the overall fitness of sexual populations, and genomic comparisons have shown that sexual selection can lead to accelerated evolution. Here, we examine the advantages of dioecy versus hermaphroditism by comparing the rate of evolution in sex-related genes and the rate of accumulation of deleterious mutations using a large number of orthologs (11,493) in the dioecious Caenorhabditis remanei and the hermaphroditic Caenorhabditis briggsae. We have used this data set to estimate the deleterious mutation rate per generation, U, in both species and find that although it is significantly higher in hermaphrodites, both species are at least 2 orders of magnitude lower than the value required to explain the persistence of sex by efficiency at purging deleterious mutations alone. We also find that genes expressed in sperm are evolving rapidly in both species; however, they show a greater increase in their rate of evolution relative to genes expressed in other tissues in C. remanei, suggesting stronger sexual selection pressure acting on these genes in dioecious species. Interestingly, the persistence of a signal of rapid evolution of sperm genes in C. briggsae suggests a recent evolutionary origin of hermaphrodism in this lineage. Our results provide empirical evidence of increased sexual selection pressure in dioecious animals, supporting the possibility that sexual selection may play an important role in the maintenance of sexual reproduction.

Gene networks, occlusal clocks, and functional patches: new understanding of pattern and process in the evolution of the dentition.

PubMed

Polly, P David

2015-05-01

Our understanding of the evolution of the dentition has been transformed by advances in the developmental biology, genetics, and functional morphology of teeth, as well as the methods available for studying tooth form and function. The hierarchical complexity of dental developmental genetics combined with dynamic effects of cells and tissues during development allow for substantial, rapid, and potentially non-linear evolutionary changes. Studies of selection on tooth function in the wild and evolutionary functional comparisons both suggest that tooth function and adaptation to diets are the most important factors guiding the evolution of teeth, yet selection against random changes that produce malocclusions (selectional drift) may be an equally important factor in groups with tribosphenic dentitions. These advances are critically reviewed here.

Rapid divergence of histones in Hydrozoa (Cnidaria) and evolution of a novel histone involved in DNA damage response in hydra.

PubMed

Reddy, Puli Chandramouli; Ubhe, Suyog; Sirwani, Neha; Lohokare, Rasika; Galande, Sanjeev

2017-08-01

Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra. Here, we report identification of the complete repertoire of histone-coding genes in the Hydra magnipapillata genome. Hydra histones were classified based on their copy numbers, gene structure and other characteristic features. Genomic organization of canonical histone genes revealed the presence of H2A-H2B and H3-H4 paired clusters in high frequency and also a cluster with all core histones along with H1. Phylogenetic analysis of identified members of H2A and H2B histones suggested rapid expansion of these groups in Hydrozoa resulting in the appearance of unique subtypes. Amino acid sequence level comparisons of H2A and H2B forms with bilaterian counterparts suggest the possibility of a highly mobile nature of nucleosomes in hydra. Absolute quantitation of transcripts confirmed the high copy number of histones and supported the canonical nature of H2A. Furthermore, functional characterization of H2A.X.1 and a unique variant H2A.X.2 in the gastric region suggest their role in the maintenance of genome integrity and differentiation processes. These findings provide insights into the evolution of histones and their variants in hydra. Copyright © 2017 Elsevier GmbH. All rights reserved.

Rapid evolution of the intersexual genetic correlation for fitness in Drosophila melanogaster

PubMed Central

Collet, Julie M.; Fuentes, Sara; Hesketh, Jack; Hill, Mark S.; Innocenti, Paolo; Morrow, Edward H.; Fowler, Kevin; Reuter, Max

2016-01-01

Sexual antagonism (SA) arises when male and female phenotypes are under opposing selection, yet genetically correlated. Until resolved, antagonism limits evolution toward optimal sex‐specific phenotypes. Despite its importance for sex‐specific adaptation and existing theory, the dynamics of SA resolution are not well understood empirically. Here, we present data from Drosophila melanogaster, compatible with a resolution of SA. We compared two independent replicates of the “LHM” population in which SA had previously been described. Both had been maintained under identical, controlled conditions, and separated for around 200 generations. Although heritabilities of male and female fitness were similar, the intersexual genetic correlation differed significantly, being negative in one replicate (indicating SA) but close to zero in the other. Using population sequencing, we show that phenotypic differences were associated with population divergence in allele frequencies at nonrandom loci across the genome. Large frequency changes were more prevalent in the population without SA and were enriched at loci mapping to genes previously shown to have sexually antagonistic relationships between expression and fitness. Our data suggest that rapid evolution toward SA resolution has occurred in one of the populations and open avenues toward studying the genetics of SA and its resolution. PMID:27077679

Fluctuating Hydrodynamics Confronts the Rapidity Dependence of Transverse Momentum Fluctuations

NASA Astrophysics Data System (ADS)

Pokharel, Rajendra; Gavin, Sean; Moschelli, George

2012-10-01

Interest in the development of the theory of fluctuating hydrodynamics is growing [1]. Early efforts suggested that viscous diffusion broadens the rapidity dependence of transverse momentum correlations [2]. That work stimulated an experimental analysis by STAR [3]. We attack this new data along two fronts. First, we compute STAR's fluctuation observable using the NeXSPheRIO code, which combines fluctuating initial conditions from a string fragmentation model with deterministic viscosity-free hydrodynamic evolution. We find that NeXSPheRIO produces a longitudinal narrowing, in contrast to the data. Second, we study the hydrodynamic evolution using second order causal viscous hydrodynamics including Langevin noise. We obtain a deterministic evolution equation for the transverse momentum density correlation function. We use the latest theoretical equations of state and transport coefficients to compute STAR's observable. The results are in excellent accord with the measured broadening. In addition, we predict features of the distribution that can distinguish 2nd and 1st order diffusion. [4pt] [1] J. Kapusta, B. Mueller, M. Stephanov, arXiv:1112.6405 [nucl-th].[0pt] [2] S. Gavin and M. Abdel-Aziz, Phys. Rev. Lett. 97, 162302 (2006)[0pt] [3] H. Agakishiev et al., STAR, STAR, Phys. Lett. B704

HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.

PubMed

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F; McMichael, Andrew; Shaw, George M; Hahn, Beatrice H; Korber, Bette; Seoighe, Cathal

2009-05-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections.

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

PubMed Central

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F.; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F.; McMichael, Andrew; Shaw, George M.; Hahn, Beatrice H.; Korber, Bette; Seoighe, Cathal

2009-01-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections. PMID:19424423

Extensive morphological divergence and rapid evolution of the larval neuromuscular junction in Drosophila.

PubMed

Campbell, Megan; Ganetzky, Barry

2012-03-13

Although the complexity and circuitry of nervous systems undergo evolutionary change, we lack understanding of the general principles and specific mechanisms through which it occurs. The Drosophila larval neuromuscular junction (NMJ), which has been widely used for studies of synaptic development and function, is also an excellent system for studies of synaptic evolution because the genus spans >40 Myr of evolution and the same identified synapse can be examined across the entire phylogeny. We have now characterized morphology of the NMJ on muscle 4 (NMJ4) in >20 species of Drosophila. Although there is little variation within a species, NMJ morphology and complexity vary extensively between species. We find no significant correlation between NMJ phenotypes and phylogeny for the species examined, suggesting that drift alone cannot explain the phenotypic variation and that selection likely plays an important role. However, the nature of the selective pressure is still unclear because basic parameters of synaptic function remain uniform. Whatever the mechanism, NMJ morphology is evolving rapidly in comparison with other morphological features because NMJ phenotypes differ even between several sibling species pairs. The discovery of this unexpectedly extensive divergence in NMJ morphology among Drosophila species provides unique opportunities to investigate mechanisms that regulate synaptic growth; the interrelationships between synaptic morphology, neural function, and behavior; and the evolution of nervous systems and behavior in natural populations.

The temporal evolution of explosive events and its implication on reconnection dynamics

NASA Astrophysics Data System (ADS)

Guo, L.; Liu, W.; De Pontieu, B.; Huang, Y. M.; Peter, H.; Bhattacharjee, A.

2017-12-01

Transition-region explosive events and other bursts seen in extreme UV light are characterized by broad spectral line profiles, and the more violent ones show a strong enhancement of emission. They are thought to be driven by magnetic reconnection, because of their characteristic spectral profiles often indicating strong Alfvénic flows, and because of the fact that they typically occur where magnetic flux concentrations of opposite polarity intersect. In this presentation, we will focus on the temporal evolution of transition-region explosive events. In particular, we will investigate fast onsets of these events and the rapid oscillations of intensity during these event. The fast onset refers to the beginning of an explosive event, where the intensities and the widths of its line profiles increase dramatically (often within less than 10 seconds) and the rapid oscillations of intensity refer to blinks of emission that usually last less than 10 seconds during the event. In order to interpret and understand underlying mechanisms of these observations, we conduct numerical simulation of an explosive event and calculate its spectra. We observe a similar temporal evolution in the synthetic Si IV spectra when the explosive event is driven by time-dependent reconnection—plasmoid instability. The qualitative agreement between observations and simulations suggests that the temporal evolution of Si IV spectra of explosive events are closely related to reconnection dynamics.

Ecotype-specific and chromosome-specific expansion of variant centromeric satellites in Arabidopsis thaliana.

PubMed

Ito, Hidetaka; Miura, Asuka; Takashima, Kazuya; Kakutani, Tetsuji

2007-01-01

Despite the conserved roles and conserved protein machineries of centromeres, their nucleotide sequences can be highly diverse even among related species. The diversity reflects rapid evolution, but the underlying mechanism is largely unknown. One approach to monitor rapid evolution is examination of intra-specific variation. Here we report variant centromeric satellites of Arabidopsis thaliana found through survey of 103 natural accessions (ecotypes). Among them, a cluster of variant centromeric satellites was detected in one ecotype, Cape Verde Islands (Cvi). Recombinant inbred mapping revealed that the variant satellites are distributed in centromeric region of the chromosome 5 (CEN5) of this ecotype. This apparently recent variant accumulation is associated with large deletion of a pericentromeric region and the expansion of satellite region. The variant satellite was bound to HTR12 (centromeric variant histone H3), although expansion of the satellite was not associated with comparable increase in the HTR12 binding. The results suggest that variant satellites with centromere function can rapidly accumulate in one centromere, supporting the model that the satellite repeats in the array are homogenized by occasional unequal crossing-over, which has a potential to generate an expansion of local sequence variants within a centromere cluster.

Multiple shifts to different pollinators fuelled rapid diversification in sexually deceptive Ophrys orchids.

PubMed

Breitkopf, Hendrik; Onstein, Renske E; Cafasso, Donata; Schlüter, Philipp M; Cozzolino, Salvatore

2015-07-01

Episodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys). Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework. It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history. Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Rapid rate of control-region evolution in Pacific butterflyfishes (Chaetodontidae).

PubMed

McMillan, W O; Palumbi, S R

1997-11-01

Sequence differences in the tRNA-proline (tRNApro) end of the mitochondrial control-region of three species of Pacific butterflyfishes accumulated 33-43 times more rapidly than did changes within the mitochondrial cytochrome b gene (cytb). Rapid evolution in this region was accompanied by strong transition/transversion bias and large variation in the probability of a DNA substitution among sites. These substitution constraints placed an absolute ceiling on the magnitude of sequence divergence that could be detected between individuals. This divergence "ceiling" was reached rapidly and led to a decay in the relative rate of control-region/cytb b evolution. A high rate of evolution in this section of the control-region of butterflyfishes stands in marked contrast to the patterns reported in some other fish lineages. Although the mechanism underlying rate variation remains unclear, all taxa with rapid evolution in the 5'-end of the control-region showed extreme transition biases. By contrast, in taxa with slower control-region evolution, transitions accumulated at nearly the same rate as transversions. More information is needed to understand the relationship between nucleotide bias and the rate of evolution in the 5'-end of the control-region. Despite strong constraints on sequence change, phylogenetic information was preserved in the group of recently differentiated species and supported the clustering of sequences into three major mtDNA groupings. Within these groups, very similar control-region sequences were widely distributed across the Pacific Ocean and were shared between recognized species, indicating a lack of mitochondrial sequence monophyly among species.

Genetics of Cerebellar and Neocortical Expansion in Anthropoid Primates: A Comparative Approach

PubMed Central

Harrison, Peter W.; Montgomery, Stephen H.

2017-01-01

What adaptive changes in brain structure and function underpin the evolution of increased cognitive performance in humans and our close relatives? Identifying the genetic basis of brain evolution has become a major tool in answering this question. Numerous cases of positive selection, altered gene expression or gene duplication have been identified that may contribute to the evolution of the neocortex, which is widely assumed to play a predominant role in cognitive evolution. However, the components of the neocortex co-evolve with other functionally interdependent regions of the brain, most notably in the cerebellum. The cerebellum is linked to a range of cognitive tasks and expanded rapidly during hominoid evolution. Here we present data that suggest that, across anthropoid primates, protein-coding genes with known roles in cerebellum development were just as likely to be targeted by selection as genes linked to cortical development. Indeed, based on currently available gene ontology data, protein-coding genes with known roles in cerebellum development are more likely to have evolved adaptively during hominoid evolution. This is consistent with phenotypic data suggesting an accelerated rate of cerebellar expansion in apes that is beyond that predicted from scaling with the neocortex in other primates. Finally, we present evidence that the strength of selection on specific genes is associated with variation in the volume of either the neocortex or the cerebellum, but not both. This result provides preliminary evidence that co-variation between these brain components during anthropoid evolution may be at least partly regulated by selection on independent loci, a conclusion that is consistent with recent intraspecific genetic analyses and a mosaic model of brain evolution that predicts adaptive evolution of brain structure. PMID:28683440

Evolution in an extreme environment: developmental biases and phenotypic integration in the adaptive radiation of antarctic notothenioids.

PubMed

Hu, Yinan; Ghigliotti, Laura; Vacchi, Marino; Pisano, Eva; Detrich, H William; Albertson, R Craig

2016-06-29

Over the past 40 million years water temperatures have dramatically dropped in the Southern Ocean, which has led to the local extinction of most nearshore fish lineages. The evolution of antifreeze glycoproteins in notothenioids, however, enabled these ancestrally benthic fishes to survive and adapt as temperatures reached the freezing point of seawater (-1.86 °C). Antarctic notothenioids now represent the primary teleost lineage in the Southern Ocean and are of fundamental importance to the local ecosystem. The radiation of notothenioids has been fostered by the evolution of "secondary pelagicism", the invasion of pelagic habitats, as the group diversified to fill newly available foraging niches in the water column. While elaborate craniofacial modifications have accompanied this adaptive radiation, little is known about how these morphological changes have contributed to the evolutionary success of notothenioids. We used a 3D-morphometrics approach to investigate patterns of morphological variation in the craniofacial skeleton among notothenioids, and show that variation in head shape is best explained by divergent selection with respect to foraging niche. We document further an accelerated rate of morphological evolution in the icefish family Channichthyidae, and show that their rapid diversification was accompanied by the evolution of relatively high levels of morphological integration. Whereas most studies suggest that extensive integration should constrain phenotypic evolution, icefish stand out as a rare example of increased integration possibly facilitating evolutionary potential. Finally, we show that the unique feeding apparatus in notothenioids in general, and icefish in particular, can be traced to shifts in early developmental patterning mechanisms and ongoing growth of the pharyngeal skeleton. Our work suggests that ecological opportunity is a major factor driving craniofacial variation in this group. Further, the observation that closely related lineages can differ dramatically in integration suggests that this trait can evolve quickly. We propose that the evolution of high levels of phenotypic integration in icefishes may be considered a key innovation that facilitated their morphological evolution and subsequent ecological expansion.

Changing selective pressure during antigenic changes in human influenza H3.

PubMed

Blackburne, Benjamin P; Hay, Alan J; Goldstein, Richard A

2008-05-02

The rapid evolution of influenza viruses presents difficulties in maintaining the optimal efficiency of vaccines. Amino acid substitutions result in antigenic drift, a process whereby antisera raised in response to one virus have reduced effectiveness against future viruses. Interestingly, while amino acid substitutions occur at a relatively constant rate, the antigenic properties of H3 move in a discontinuous, step-wise manner. It is not clear why this punctuated evolution occurs, whether this represents simply the fact that some substitutions affect these properties more than others, or if this is indicative of a changing relationship between the virus and the host. In addition, the role of changing glycosylation of the haemagglutinin in these shifts in antigenic properties is unknown. We analysed the antigenic drift of HA1 from human influenza H3 using a model of sequence change that allows for variation in selective pressure at different locations in the sequence, as well as at different parts of the phylogenetic tree. We detect significant changes in selective pressure that occur preferentially during major changes in antigenic properties. Despite the large increase in glycosylation during the past 40 years, changes in glycosylation did not correlate either with changes in antigenic properties or with significantly more rapid changes in selective pressure. The locations that undergo changes in selective pressure are largely in places undergoing adaptive evolution, in antigenic locations, and in locations or near locations undergoing substitutions that characterise the change in antigenicity of the virus. Our results suggest that the relationship of the virus to the host changes with time, with the shifts in antigenic properties representing changes in this relationship. This suggests that the virus and host immune system are evolving different methods to counter each other. While we are able to characterise the rapid increase in glycosylation of the haemagglutinin during time in human influenza H3, an increase not present in influenza in birds, this increase seems unrelated to the observed changes in antigenic properties.

Turn-taking in Human Communication--Origins and Implications for Language Processing.

PubMed

Levinson, Stephen C

2016-01-01

Most language usage is interactive, involving rapid turn-taking. The turn-taking system has a number of striking properties: turns are short and responses are remarkably rapid, but turns are of varying length and often of very complex construction such that the underlying cognitive processing is highly compressed. Although neglected in cognitive science, the system has deep implications for language processing and acquisition that are only now becoming clear. Appearing earlier in ontogeny than linguistic competence, it is also found across all the major primate clades. This suggests a possible phylogenetic continuity, which may provide key insights into language evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

The evolution and ascent paths of mantle xenolith-bearing magma: Observations and insights from Cenozoic basalts in Southeast China

NASA Astrophysics Data System (ADS)

Sun, Pu; Niu, Yaoling; Guo, Pengyuan; Cui, Huixia; Ye, Lei; Liu, Jinju

2018-06-01

Studies have shown that mantle xenolith-bearing magmas must ascend rapidly to carry mantle xenoliths to the surface. It has thus been inferred inadvertently that such rapid ascending melt must have undergone little crystallization or evolution. However, this inference is apparently inconsistent with the widespread observation that xenolith-bearing alkali basalts are variably evolved with Mg# ≤72. In this paper, we discuss this important, yet overlooked, petrological problem and offer new perspectives with evidence. We analyzed the Cenozoic mantle xenolith-bearing alkali basalts from several locations in Southeast China that have experienced varying degrees of fractional crystallization (Mg# = 48-67). The variably evolved composition of host alkali basalts is not in contradiction with rapid ascent, but rather reflects inevitability of crystallization during ascent. Thermometry calculations for clinopyroxene (Cpx) megacrysts give equilibrium temperatures of 1238-1390 °C, which is consistent with the effect of conductive cooling and melt crystallization during ascent because TMelt > TLithosphere. The equilibrium pressure (18-27 kbar) of these Cpx megacrysts suggests that the crystallization takes place under lithospheric mantle conditions. The host melt must have experienced limited low-pressure residence in the shallower levels of lithospheric mantle and crust. This is in fact consistent with the rapid ascent of the host melt to bring mantle xenoliths to the surface.

Morphological adaptation influences the evolution of a mating signal.

PubMed

Ballentine, Barbara

2006-09-01

Theory predicts that forces of natural selection can reduce the intensity of sexually selected traits. In this study, I investigate how morphological adaptation to feeding ecology influences a mating signal. In birds, changes in feeding ecology can cause rapid divergence in bill morphology. Because bills are also important for song production, feeding ecology may influence song divergence. During song, birds can rapidly change vocal tract resonance using bill movement, yet are constrained in rate and magnitude of bill movements resulting in a trade-off between trill rate and frequency bandwidth. Male swamp sparrows vary in their ability to produce rapid, broad-band trills and females prefer more physically demanding songs. Populations of swamp sparrows adapted to the feeding ecology of tidal marshes have larger bills than inland populations. Larger bills should increase the constraints of producing rapid, broad-band trills allowing for a test of how changes in feeding ecology affect a feature of song used in mate choice. I found significant differences in acoustic features of song consistent with the hypothesis that coastal males are less able to meet the physical demands of song production because of the constraints of having larger bills. As possible compensation for decreases in song performance, coastal populations exhibit an increase in song complexity. These changes support the current model of how motor constraints influence song production and suggest a mechanism by which feeding ecology can influence signal evolution.

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kohler, Annegret; Kuo, Alan; Nagy, Laszlo G.

To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergentmore » evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.« less

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

DOE PAGES

Kohler, Annegret; Kuo, Alan; Nagy, Laszlo G.; ...

2015-02-23

To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergentmore » evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.« less

Chemical Evolution of Ozone and Its Precursors in Asian Pacific Rim Outflow During TRACE-P

NASA Astrophysics Data System (ADS)

Hamlin, A.; Crawford, J.; Olson, J.; Pippin, M.; Avery, M.; Sachse, G.; Barrick, J.; Blake, D.; Tan, D.; Sandholm, S.; Kondo, Y.; Singh, H.; Eisele, F.; Zondlo, M.; Flocke, F.; Talbot, R.

2002-12-01

During NASA's GTE/TRACE-P (Transport and Chemical Evolution over the Pacific) mission, a widespread stagnant pollution layer was observed between 2 and 4 km over the central Pacific. In this region, high levels of O3 (70~ppbv), CO (210~ppbv), and NOx (130~pptv) were observed. Back trajectories suggest this airmass had been rapidly transported from the Asian coast near the Yellow Sea to the central Pacific where it underwent subsidence. The chemical evolution of ozone and its precursors for this airmass is examined using lagrangian photochemical box model calculations. Simulations are conducted along trajectories which intersect the flight path where predicted mixing ratios are compared to measurements. An analysis of the photochemical processes controlling the cycling of nitrogen oxides and ozone production and destruction during transport will be presented.

Sexual selection drives evolution and rapid turnover of male gene expression.

PubMed

Harrison, Peter W; Wright, Alison E; Zimmer, Fabian; Dean, Rebecca; Montgomery, Stephen H; Pointer, Marie A; Mank, Judith E

2015-04-07

The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.

Cenozoic Tectonic Evolution of Northeast China and Surrounding Areas Reproduced by Slab Subduction Models

NASA Astrophysics Data System (ADS)

Yang, T.; Moresi, L. N.; Zhao, D.; Sandiford, D.

2017-12-01

Northeast China lies at the continental margin of the western Pacific subduction zone where the Pacific Plate subducts beneath the Eurasia Plate along the Kuril-Japan trench during the Cenozoic, after the consumption of the Izanagi Plate. The Izanagi Plate and the Izanagi-Pacific mid-ocean ridge recycled to the mantle beneath Eurasia before the early Cenozoic. Plate reconstructions suggest that (1) age of the incoming Pacific Plate at the trench increases with time; (2) convergence rate between the Pacific and Eurasia Plates increased rapidly from the late Eocene to the early Miocene. Northeast China and surrounding areas suffered widespread extension and magmatism during the Cenozoic, culminating in the opening of the Japan Sea and the rifting of the Baikal Rift Zone. The Japan Sea opened during the early Miocene and kept spreading until the late Miocene, since when compression tectonics gradually prevailed. The Baikal Rift Zone underwent slow extension in the Cenozoic but its extension rate has increased rapidly since the late Miocene. We investigate the Cenozoic tectonic evolution of Northeast China and surrounding areas with geodynamic models. Our study suggests that the rapid aging of the incoming Pacific Plate at the subduction zone leads to the increase of plate convergence and trench motion rates, and explains the observed sequence of regional tectonic events. Our geodynamic model, which reproduces the Cenozoic regional tectonic events, predicts slab morphology and stress state consistent with seismic observations, including over 1000 km of slab stagnant in the transition zone, and the along-dip principal compressional stress direction. Our model requires a value of the 660 km phase transition Clapeyron slope of -2.5 MPa/K to reproduce the stagnant slab and tectonic events in the study region. This suggests that the Pacific slab is hydrated in the transition zone, explaining geochemical characteristics of some regional Cenozoic igneous rocks which were suggested to originate from a hydrous mantle transition zone.

Flight Planning for the International Space Station-Levitation Observation of Dendrite Evolution in Steel Ternary Alloy Rapid Solidification

NASA Technical Reports Server (NTRS)

Flemings, M. C.; Matson, D. M.; Loser, W.; Hyers, R. W.; Rogers, J. R.; Curreri, Peter A. (Technical Monitor)

2002-01-01

The paper is an overview of the status and science for the LODESTARS research project. The program is aimed at understanding how melt convection influences phase selection and the evolution of rapid solidification microstructures

The 1983 hydraulic jump in Crystal Rapid: implications for river- running and geomorphic evolution in the Grand Canyon.

USGS Publications Warehouse

Kieffer, S.W.

1985-01-01

At Crystal Creek, a debris fan was emplaced in 1966, constricting the channel of the Colorado River to about 0.25 of its upstream width between 1967 and 1983, forming a major rapid. The hydraulics of Crystal Creek rapid are described, and an analysis is presented to support the hypothesis that the major wave in the rapid was a normal wave (one type of hydraulic jump). Hydraulic jumps rarely occur in natural river channels with erodible beds, but one was present at Crystal Rapid because of the unusually severe constriction of the Colorado River by the 1966 debris fan. A quantitative model for river debris fan shapes is proposed and is used to estimate prehistoric flood levels from the observed constrictions: the 0.5 value of river constriction found at the more mature debris fans in the Grand Canyon suggests that peak flood discharges of approximately 11 320 m3/s have occurred. -from Author

Lineage tracing reveals multipotent stem cells maintain human adenomas and the pattern of clonal expansion in tumor evolution

PubMed Central

Humphries, Adam; Cereser, Biancastella; Gay, Laura J.; Miller, Daniel S. J.; Das, Bibek; Gutteridge, Alice; Elia, George; Nye, Emma; Jeffery, Rosemary; Poulsom, Richard; Novelli, Marco R.; Rodriguez-Justo, Manuel; McDonald, Stuart A. C.; Wright, Nicholas A.; Graham, Trevor A.

2013-01-01

The genetic and morphological development of colorectal cancer is a paradigm for tumorigenesis. However, the dynamics of clonal evolution underpinning carcinogenesis remain poorly understood. Here we identify multipotential stem cells within human colorectal adenomas and use methylation patterns of nonexpressed genes to characterize clonal evolution. Numerous individual crypts from six colonic adenomas and a hyperplastic polyp were microdissected and characterized for genetic lesions. Clones deficient in cytochrome c oxidase (CCO−) were identified by histochemical staining followed by mtDNA sequencing. Topographical maps of clone locations were constructed using a combination of these data. Multilineage differentiation within clones was demonstrated by immunofluorescence. Methylation patterns of adenomatous crypts were determined by clonal bisulphite sequencing; methylation pattern diversity was compared with a mathematical model to infer to clonal dynamics. Individual adenomatous crypts were clonal for mtDNA mutations and contained both mucin-secreting and neuroendocrine cells, demonstrating that the crypt contained a multipotent stem cell. The intracrypt methylation pattern was consistent with the crypts containing multiple competing stem cells. Adenomas were epigenetically diverse populations, suggesting that they were relatively mitotically old populations. Intratumor clones typically showed less diversity in methylation pattern than the tumor as a whole. Mathematical modeling suggested that recent clonal sweeps encompassing the whole adenoma had not occurred. Adenomatous crypts within human tumors contain actively dividing stem cells. Adenomas appeared to be relatively mitotically old populations, pocketed with occasional newly generated subclones that were the result of recent rapid clonal expansion. Relative stasis and occasional rapid subclone growth may characterize colorectal tumorigenesis. PMID:23766371

Lineage tracing reveals multipotent stem cells maintain human adenomas and the pattern of clonal expansion in tumor evolution.

PubMed

Humphries, Adam; Cereser, Biancastella; Gay, Laura J; Miller, Daniel S J; Das, Bibek; Gutteridge, Alice; Elia, George; Nye, Emma; Jeffery, Rosemary; Poulsom, Richard; Novelli, Marco R; Rodriguez-Justo, Manuel; McDonald, Stuart A C; Wright, Nicholas A; Graham, Trevor A

2013-07-02

The genetic and morphological development of colorectal cancer is a paradigm for tumorigenesis. However, the dynamics of clonal evolution underpinning carcinogenesis remain poorly understood. Here we identify multipotential stem cells within human colorectal adenomas and use methylation patterns of nonexpressed genes to characterize clonal evolution. Numerous individual crypts from six colonic adenomas and a hyperplastic polyp were microdissected and characterized for genetic lesions. Clones deficient in cytochrome c oxidase (CCO(-)) were identified by histochemical staining followed by mtDNA sequencing. Topographical maps of clone locations were constructed using a combination of these data. Multilineage differentiation within clones was demonstrated by immunofluorescence. Methylation patterns of adenomatous crypts were determined by clonal bisulphite sequencing; methylation pattern diversity was compared with a mathematical model to infer to clonal dynamics. Individual adenomatous crypts were clonal for mtDNA mutations and contained both mucin-secreting and neuroendocrine cells, demonstrating that the crypt contained a multipotent stem cell. The intracrypt methylation pattern was consistent with the crypts containing multiple competing stem cells. Adenomas were epigenetically diverse populations, suggesting that they were relatively mitotically old populations. Intratumor clones typically showed less diversity in methylation pattern than the tumor as a whole. Mathematical modeling suggested that recent clonal sweeps encompassing the whole adenoma had not occurred. Adenomatous crypts within human tumors contain actively dividing stem cells. Adenomas appeared to be relatively mitotically old populations, pocketed with occasional newly generated subclones that were the result of recent rapid clonal expansion. Relative stasis and occasional rapid subclone growth may characterize colorectal tumorigenesis.

Mitochondrial genomes suggest rapid evolution of dwarf California Channel Islands foxes (Urocyon littoralis).

PubMed

Hofman, Courtney A; Rick, Torben C; Hawkins, Melissa T R; Funk, W Chris; Ralls, Katherine; Boser, Christina L; Collins, Paul W; Coonan, Tim; King, Julie L; Morrison, Scott A; Newsome, Seth D; Sillett, T Scott; Fleischer, Robert C; Maldonado, Jesus E

2015-01-01

Island endemics are typically differentiated from their mainland progenitors in behavior, morphology, and genetics, often resulting from long-term evolutionary change. To examine mechanisms for the origins of island endemism, we present a phylogeographic analysis of whole mitochondrial genomes from the endangered island fox (Urocyon littoralis), endemic to California's Channel Islands, and mainland gray foxes (U. cinereoargenteus). Previous genetic studies suggested that foxes first appeared on the islands >16,000 years ago, before human arrival (~13,000 cal BP), while archaeological and paleontological data supported a colonization >7000 cal BP. Our results are consistent with initial fox colonization of the northern islands probably by rafting or human introduction ~9200-7100 years ago, followed quickly by human translocation of foxes from the northern to southern Channel Islands. Mitogenomes indicate that island foxes are monophyletic and most closely related to gray foxes from northern California that likely experienced a Holocene climate-induced range shift. Our data document rapid morphological evolution of island foxes (in ~2000 years or less). Despite evidence for bottlenecks, island foxes have generated and maintained multiple mitochondrial haplotypes. This study highlights the intertwined evolutionary history of island foxes and humans, and illustrates a new approach for investigating the evolutionary histories of other island endemics.

Comparative genomics using microarrays reveals divergence and loss of virulence-associated genes in host-specific strains of the insect pathogen Metarhizium anisopliae.

PubMed

Wang, Sibao; Leclerque, Andreas; Pava-Ripoll, Monica; Fang, Weiguo; St Leger, Raymond J

2009-06-01

Many strains of Metarhizium anisopliae have broad host ranges, but others are specialists and adapted to particular hosts. Patterns of gene duplication, divergence, and deletion in three generalist and three specialist strains were investigated by heterologous hybridization of genomic DNA to genes from the generalist strain Ma2575. As expected, major life processes are highly conserved, presumably due to purifying selection. However, up to 7% of Ma2575 genes were highly divergent or absent in specialist strains. Many of these sequences are conserved in other fungal species, suggesting that there has been rapid evolution and loss in specialist Metarhizium genomes. Some poorly hybridizing genes in specialists were functionally coordinated, indicative of reductive evolution. These included several involved in toxin biosynthesis and sugar metabolism in root exudates, suggesting that specialists are losing genes required to live in alternative hosts or as saprophytes. Several components of mobile genetic elements were also highly divergent or lost in specialists. Exceptionally, the genome of the specialist cricket pathogen Ma443 contained extra insertion elements that might play a role in generating evolutionary novelty. This study throws light on the abundance of orphans in genomes, as 15% of orphan sequences were found to be rapidly evolving in the Ma2575 lineage.

Mitochondrial Genomes Suggest Rapid Evolution of Dwarf California Channel Islands Foxes (Urocyon littoralis)

PubMed Central

Hofman, Courtney A.; Rick, Torben C.; Hawkins, Melissa T. R.; Funk, W. Chris; Ralls, Katherine; Boser, Christina L.; Collins, Paul W.; Coonan, Tim; King, Julie L.; Morrison, Scott A.; Newsome, Seth D.; Sillett, T. Scott; Fleischer, Robert C.; Maldonado, Jesus E.

2015-01-01

Island endemics are typically differentiated from their mainland progenitors in behavior, morphology, and genetics, often resulting from long-term evolutionary change. To examine mechanisms for the origins of island endemism, we present a phylogeographic analysis of whole mitochondrial genomes from the endangered island fox (Urocyon littoralis), endemic to California’s Channel Islands, and mainland gray foxes (U. cinereoargenteus). Previous genetic studies suggested that foxes first appeared on the islands >16,000 years ago, before human arrival (~13,000 cal BP), while archaeological and paleontological data supported a colonization >7000 cal BP. Our results are consistent with initial fox colonization of the northern islands probably by rafting or human introduction ~9200–7100 years ago, followed quickly by human translocation of foxes from the northern to southern Channel Islands. Mitogenomes indicate that island foxes are monophyletic and most closely related to gray foxes from northern California that likely experienced a Holocene climate-induced range shift. Our data document rapid morphological evolution of island foxes (in ~2000 years or less). Despite evidence for bottlenecks, island foxes have generated and maintained multiple mitochondrial haplotypes. This study highlights the intertwined evolutionary history of island foxes and humans, and illustrates a new approach for investigating the evolutionary histories of other island endemics. PMID:25714775

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

PubMed

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2014-12-12

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. Copyright © 2014, American Association for the Advancement of Science.

Recent advances in understanding the role of nutrition in human genome evolution.

PubMed

Ye, Kaixiong; Gu, Zhenglong

2011-11-01

Dietary transitions in human history have been suggested to play important roles in the evolution of mankind. Genetic variations caused by adaptation to diet during human evolution could have important health consequences in current society. The advance of sequencing technologies and the rapid accumulation of genome information provide an unprecedented opportunity to comprehensively characterize genetic variations in human populations and unravel the genetic basis of human evolution. Series of selection detection methods, based on various theoretical models and exploiting different aspects of selection signatures, have been developed. Their applications at the species and population levels have respectively led to the identification of human specific selection events that distinguish human from nonhuman primates and local adaptation events that contribute to human diversity. Scrutiny of candidate genes has revealed paradigms of adaptations to specific nutritional components and genome-wide selection scans have verified the prevalence of diet-related selection events and provided many more candidates awaiting further investigation. Understanding the role of diet in human evolution is fundamental for the development of evidence-based, genome-informed nutritional practices in the era of personal genomics.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

PubMed Central

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2015-01-01

To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

The evolution of courtship behaviors through the origination of a new gene in Drosophila

PubMed Central

Dai, Hongzheng; Chen, Ying; Chen, Sidi; Mao, Qiyan; Kennedy, David; Landback, Patrick; Eyre-Walker, Adam; Du, Wei; Long, Manyuan

2008-01-01

New genes can originate by the combination of sequences from unrelated genes or their duplicates to form a chimeric structure. These chimeric genes often evolve rapidly, suggesting that they undergo adaptive evolution and may therefore be involved in novel phenotypes. Their functions, however, are rarely known. Here, we describe the phenotypic effects of a chimeric gene, sphinx, that has recently evolved in Drosophila melanogaster. We show that a knockout of this gene leads to increased male–male courtship in D. melanogaster, although it leaves other aspects of mating behavior unchanged. Comparative studies of courtship behavior in other closely related Drosophila species suggest that this mutant phenotype of male–male courtship is the ancestral condition because these related species show much higher levels of male–male courtship than D. melanogaster. D. melanogaster therefore seems to have evolved in its courtship behaviors by the recruitment of a new chimeric gene. PMID:18508971

DEVELOPMENT OF CHINESE HEALTH LAW: OVERVIEW AND SUGGESTIONS.

PubMed

Liu, Kai; Tang, Daolu

2014-07-01

Health law is a rapidly developing law specialty in China. This article examines the current overall framework and evolution of Chinese health law, as a background to an analysis of the advantages and disadvantages of this legal regime. Research suggests that: 1) The independent status of Chinese health law as jurisprudence and a specialty ought to be assured altogether; 2) The convergence between health law and other laws should be strengthened; 3) The current Chinese health law framework ought to be completed. This suggests the necessity to find ways to improve the independence of health law in China by eliminating the convergence and completing the legal framework.

Clownfishes evolution below and above the species level

PubMed Central

Litsios, Glenn; Faye, Laurélène; Salamin, Nicolas

2018-01-01

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels. PMID:29467260

The evolution of reduced antagonism--A role for host-parasite coevolution.

PubMed

Gibson, A K; Stoy, K S; Gelarden, I A; Penley, M J; Lively, C M; Morran, L T

2015-11-01

Why do some host-parasite interactions become less antagonistic over evolutionary time? Vertical transmission can select for reduced antagonism. Vertical transmission also promotes coevolution between hosts and parasites. Therefore, we hypothesized that coevolution itself may underlie transitions to reduced antagonism. To test the coevolution hypothesis, we selected for reduced antagonism between the host Caenorhabditis elegans and its parasite Serratia marcescens. This parasite is horizontally transmitted, which allowed us to study coevolution independently of vertical transmission. After 20 generations, we observed a response to selection when coevolution was possible: reduced antagonism evolved in the copassaged treatment. Reduced antagonism, however, did not evolve when hosts or parasites were independently selected without coevolution. In addition, we found strong local adaptation for reduced antagonism between replicate host/parasite lines in the copassaged treatment. Taken together, these results strongly suggest that coevolution was critical to the rapid evolution of reduced antagonism. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Sex Ratio Bias Leads to the Evolution of Sex Role Reversal in Honey Locust Beetles.

PubMed

Fritzsche, Karoline; Booksmythe, Isobel; Arnqvist, Göran

2016-09-26

The reversal of conventional sex roles was enigmatic to Darwin, who suggested that it may evolve when sex ratios are female biased [1]. Here we present direct evidence confirming Darwin's hypothesis. We investigated mating system evolution in a sex-role-reversed beetle (Megabruchidius dorsalis) using experimental evolution under manipulated sex ratios and food regimes. In female-biased populations, where reproductive competition among females was intensified, females evolved to be more attractive and the sex roles became more reversed. Interestingly, female-specific mating behavior evolved more rapidly than male-specific mating behavior. We show that sexual selection due to reproductive competition can be strong in females and can target much the same traits as in males of species with conventional mating systems. Our study highlights two central points: the role of ecology in directing sexual selection and the role that females play in mating system evolution. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolution of the human-specific microRNA miR-941

PubMed Central

Hu, Hai Yang; He, Liu; Fominykh, Kseniya; Yan, Zheng; Guo, Song; Zhang, Xiaoyu; Taylor, Martin S.; Tang, Lin; Li, Jie; Liu, Jianmei; Wang, Wen; Yu, Haijing; Khaitovich, Philipp

2012-01-01

MicroRNA-mediated gene regulation is important in many physiological processes. Here we explore the roles of a microRNA, miR-941, in human evolution. We find that miR-941 emerged de novo in the human lineage, between six and one million years ago, from an evolutionarily volatile tandem repeat sequence. Its copy-number remains polymorphic in humans and shows a trend for decreasing copy-number with migration out of Africa. Emergence of miR-941 was accompanied by accelerated loss of miR-941-binding sites, presumably to escape regulation. We further show that miR-941 is highly expressed in pluripotent cells, repressed upon differentiation and preferentially targets genes in hedgehog- and insulin-signalling pathways, thus suggesting roles in cellular differentiation. Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling. Taken together, these results implicate miR-941 in human evolution, and provide an example of rapid regulatory evolution in the human linage. PMID:23093182

Thiol-catalyzed formation of lactate and glycerate from glyceraldehyde. [significance in molecular evolution

NASA Technical Reports Server (NTRS)

Weber, A. L.

1983-01-01

The rate of lactate formation from glyceraldehyde, catalyzed by N-acetyl-cysteine at ambient temperature in aqueous sodium phosphate (pH 7.0), is more rapid at higher sodium phosphate concentrations and remains essentially the same in the presence and absence of oxygen. The dramatic increase in the rate of glycerate formation that is brought about by this thiol, N-acetylcysteine, is accompanied by commensurate decreases in the rates of glycolate and formate production. It is suggested that the thiol-dependent formation of lactate and glycerate occurs by way of their respective thioesters. Attention is given to the significance of these reactions in the context of molecular evolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stern, Adi; Sorek, Rotem

Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies. In this paper, we discuss the unique and common features of phage resistance mechanisms and their role in global biodiversity. Finally, the commonalities between defense mechanismsmore » suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.« less

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

PubMed Central

Feng, Yan-Jie; Liang, Dan; Hillis, David M.; Cannatella, David C.; Zhang, Peng

2017-01-01

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation. PMID:28673970

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary.

PubMed

Feng, Yan-Jie; Blackburn, David C; Liang, Dan; Hillis, David M; Wake, David B; Cannatella, David C; Zhang, Peng

2017-07-18

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hastings, Danielle M.; Margot, Jean-Luc; Ragozzine, Darin

Hi’iaka is the larger outer satellite of the dwarf planet Haumea. Using relative photometry from the Hubble Space Telescope and Magellan and a phase dispersion minimization analysis, we have identified the rotation period of Hi’iaka to be ∼9.8 hr (double peaked). This is ∼120 times faster than its orbital period, creating new questions about the formation of this system and possible tidal evolution. The rapid rotation suggests that Hi’iaka could have a significant obliquity and spin precession that could be visible in light curves within a few years. We then turn to an investigation of what we learn about themore » (currently unclear) formation of the Haumea system and family based on this unexpectedly rapid rotation rate. We explore the importance of the initial semimajor axis and rotation period in tidal evolution theory and find that they strongly influence the time required to despin to synchronous rotation, relevant to understanding a wide variety of satellite and binary systems. We find that despinning tides do not necessarily lead to synchronous spin periods for Hi’iaka, even if it formed near the Roche limit. Therefore, the short rotation period of Hi’iaka does not rule out significant tidal evolution. Hi’iaka’s spin period is also consistent with formation near its current location and spin-up due to Haumea-centric impactors.« less

Environmental Noise, Genetic Diversity and the Evolution of Evolvability and Robustness in Model Gene Networks

PubMed Central

Steiner, Christopher F.

2012-01-01

The ability of organisms to adapt and persist in the face of environmental change is accepted as a fundamental feature of natural systems. More contentious is whether the capacity of organisms to adapt (or “evolvability”) can itself evolve and the mechanisms underlying such responses. Using model gene networks, I provide evidence that evolvability emerges more readily when populations experience positively autocorrelated environmental noise (red noise) compared to populations in stable or randomly varying (white noise) environments. Evolvability was correlated with increasing genetic robustness to effects on network viability and decreasing robustness to effects on phenotypic expression; populations whose networks displayed greater viability robustness and lower phenotypic robustness produced more additive genetic variation and adapted more rapidly in novel environments. Patterns of selection for robustness varied antagonistically with epistatic effects of mutations on viability and phenotypic expression, suggesting that trade-offs between these properties may constrain their evolutionary responses. Evolution of evolvability and robustness was stronger in sexual populations compared to asexual populations indicating that enhanced genetic variation under fluctuating selection combined with recombination load is a primary driver of the emergence of evolvability. These results provide insight into the mechanisms potentially underlying rapid adaptation as well as the environmental conditions that drive the evolution of genetic interactions. PMID:23284934

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

PubMed Central

Dujon, Bernard

2012-01-01

Summary: Forced interspecific hybridization has been used in yeasts for many years to study speciation or to construct artificial strains with novel fermentative and metabolic properties. Recent genome analyses indicate that natural hybrids are also generated spontaneously between yeasts belonging to distinct species, creating lineages with novel phenotypes, varied genetic stability, or altered virulence in the case of pathogens. Large segmental introgressions from evolutionarily distant species are also visible in some yeast genomes, suggesting that interspecific genetic exchanges occur during evolution. The origin of this phenomenon remains unclear, but it is likely based on weak prezygotic barriers, limited Dobzhansky-Muller (DM) incompatibilities, and rapid clonal expansions. Newly formed interspecies hybrids suffer rapid changes in the genetic contribution of each parent, including chromosome loss or aneuploidy, translocations, and loss of heterozygosity, that, except in a few recently studied cases, remain to be characterized more precisely at the genomic level by use of modern technologies. We review here known cases of natural or artificially formed interspecies hybrids between yeasts and discuss their potential importance in terms of genome evolution. Problems of meiotic fertility, ploidy constraint, gene and gene product compatibility, and nucleomitochondrial interactions are discussed and placed in the context of other known mechanisms of yeast genome evolution as a model for eukaryotes. PMID:23204364

Three-Fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of Snake Venom Toxins

PubMed Central

Sunagar, Kartik; Jackson, Timothy N. W.; Undheim, Eivind A. B.; Ali, Syed. A.; Antunes, Agostinho; Fry, Bryan G.

2013-01-01

Three-finger toxins (3FTx) represent one of the most abundantly secreted and potently toxic components of colubrid (Colubridae), elapid (Elapidae) and psammophid (Psammophiinae subfamily of the Lamprophidae) snake venom arsenal. Despite their conserved structural similarity, they perform a diversity of biological functions. Although they are theorised to undergo adaptive evolution, the underlying diversification mechanisms remain elusive. Here, we report the molecular evolution of different 3FTx functional forms and show that positively selected point mutations have driven the rapid evolution and diversification of 3FTx. These diversification events not only correlate with the evolution of advanced venom delivery systems (VDS) in Caenophidia, but in particular the explosive diversification of the clade subsequent to the evolution of a high pressure, hollow-fanged VDS in elapids, highlighting the significant role of these toxins in the evolution of advanced snakes. We show that Type I, II and III α-neurotoxins have evolved with extreme rapidity under the influence of positive selection. We also show that novel Oxyuranus/Pseudonaja Type II forms lacking the apotypic loop-2 stabilising cysteine doublet characteristic of Type II forms are not phylogenetically basal in relation to other Type IIs as previously thought, but are the result of secondary loss of these apotypic cysteines on at least three separate occasions. Not all 3FTxs have evolved rapidly: κ-neurotoxins, which form non-covalently associated heterodimers, have experienced a relatively weaker influence of diversifying selection; while cytotoxic 3FTx, with their functional sites, dispersed over 40% of the molecular surface, have been extremely constrained by negative selection. We show that the a previous theory of 3FTx molecular evolution (termed ASSET) is evolutionarily implausible and cannot account for the considerable variation observed in very short segments of 3FTx. Instead, we propose a theory of Rapid Accumulation of Variations in Exposed Residues (RAVER) to illustrate the significance of point mutations, guided by focal mutagenesis and positive selection in the evolution and diversification of 3FTx. PMID:24253238

Directed evolution of cell size in Escherichia coli.

PubMed

Yoshida, Mari; Tsuru, Saburo; Hirata, Naoko; Seno, Shigeto; Matsuda, Hideo; Ying, Bei-Wen; Yomo, Tetsuya

2014-12-17

In bacteria, cell size affects chromosome replication, the assembly of division machinery, cell wall synthesis, membrane synthesis and ultimately growth rate. In addition, cell size can also be a target for Darwinian evolution for protection from predators. This strong coupling of cell size and growth, however, could lead to the introduction of growth defects after size evolution. An important question remains: can bacterial cell size change and/or evolve without imposing a growth burden? The directed evolution of particular cell sizes, without a growth burden, was tested with a laboratory Escherichia coli strain. Cells of defined size ranges were collected by a cell sorter and were subsequently cultured. This selection-propagation cycle was repeated, and significant changes in cell size were detected within 400 generations. In addition, the width of the size distribution was altered. The changes in cell size were unaccompanied by a growth burden. Whole genome sequencing revealed that only a few mutations in genes related to membrane synthesis conferred the size evolution. In conclusion, bacterial cell size could evolve, through a few mutations, without growth reduction. The size evolution without growth reduction suggests a rapid evolutionary change to diverse cell sizes in bacterial survival strategies.

Insight into winter haze formation mechanisms based on aerosol hygroscopicity and effective density measurements

NASA Astrophysics Data System (ADS)

Xie, Yuanyuan; Ye, Xingnan; Ma, Zhen; Tao, Ye; Wang, Ruyu; Zhang, Ci; Yang, Xin; Chen, Jianmin; Chen, Hong

2017-06-01

We characterize a representative particulate matter (PM) episode that occurred in Shanghai during winter 2014. Particle size distribution, hygroscopicity, effective density, and single particle mass spectrometry were determined online, along with offline analysis of water-soluble inorganic ions. The mass ratio of SNA / PM1. 0 (sulfate, nitrate, and ammonium) fluctuated slightly around 0.28, suggesting that both secondary inorganic compounds and carbonaceous aerosols contributed substantially to the haze formation, regardless of pollution level. Nitrate was the most abundant ionic species during hazy periods, indicating that NOx contributed more to haze formation in Shanghai than did SO2. During the representative PM episode, the calculated PM was always consistent with the measured PM1. 0, indicating that the enhanced pollution level was attributable to the elevated number of larger particles. The number fraction of the near-hydrophobic group increased as the PM episode developed, indicating the accumulation of local emissions. Three banana-shaped particle evolutions were consistent with the rapid increase of PM1. 0 mass loading, indicating that the rapid size growth by the condensation of condensable materials was responsible for the severe haze formation. Both hygroscopicity and effective density of the particles increased considerably with growing particle size during the banana-shaped evolutions, indicating that the secondary transformation of NOx and SO2 was one of the most important contributors to the particle growth. Our results suggest that the accumulation of gas-phase and particulate pollutants under stagnant meteorological conditions and subsequent rapid particle growth by secondary processes were primarily responsible for the haze pollution in Shanghai during wintertime.

Influence of Auroral Streamers on Rapid Evolution of Ionospheric SAPS Flows

NASA Astrophysics Data System (ADS)

Gallardo-Lacourt, Bea; Nishimura, Y.; Lyons, L. R.; Mishin, E. V.; Ruohoniemi, J. M.; Donovan, E. F.; Angelopoulos, V.; Nishitani, N.

2017-12-01

Subauroral polarization streams (SAPS) often show large, rapid enhancements above their slowly varying component. We present simultaneous observations from ground-based all-sky imagers and flows from the Super Dual Auroral Radar Network radars to investigate the relationship between auroral phenomena and flow enhancement. We first identified auroral streamers approaching the equatorward boundary of the auroral oval to examine how often the subauroral flow increased. We also performed the reverse query starting with subauroral flow enhancements and then evaluated the auroral conditions. In the forward study, 98% of the streamers approaching the equatorward boundary were associated with SAPS flow enhancements reaching 700 m/s and typically hundreds of m/s above background speeds. The reverse study reveals that flow enhancements associated with streamers (60%) and enhanced larger-scale convection (37%) contribute to SAPS flow enhancements. The strong correlation of auroral streamers with rapid evolution (approximately minutes) of SAPS flows suggests that transient fast earthward plasma sheet flows can often lead to westward SAPS flow enhancements in the subauroral region and that such enhancements are far more common than only during substorms because of the much more frequent occurrences of streamers under various geomagnetic conditions. We also found a strong correlation between flow duration and streamer duration and a weak correlation between SAPS flow velocity and streamer intensity. This result suggests that intense flow bursts in the plasma sheet (which correlate with intense streamers) are associated with intense SAPS ionospheric flows perhaps by enhancing the ring current pressure and localized pressure gradients when they are able to penetrate close enough to Earth.

Adaptive evolution of body size subject to indirect effect in trophic cascade system.

PubMed

Wang, Xin; Fan, Meng; Hao, Lina

2017-09-01

Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model. First, an eco-evolutionary model incorporating the rapid evolution is formulated to investigate the effect of rapid evolution of the consumer's body size, and to explore the impact of density-mediate indirect effect on the population dynamics and trait dynamics. Next, by employing the adaptive dynamic theory, a long-term evolutionary model of consumer body size is formulated to evaluate the effect of long-term evolution on the population dynamics and the effect of trait-mediate indirect effect. Those models admit rich dynamics that has not been observed yet in empirical studies. It is found that, both in the trait-mediated and density-mediated system, the body size of consumer in predator-consumer-resource interaction (indirect effect) evolves smaller than that in consumer-resource and predator-consumer interaction (direct effect). Moreover, in the density-mediated system, we found that the evolution of consumer body size contributes to avoiding consumer extinction (i.e., evolutionary rescue). The trait-mediate and density-mediate effects may produce opposite evolutionary response. This study suggests that the trophic cascade indirect effect affects consumer evolution, highlights a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. The modeling approaches provide avenue for study on indirect effects from an evolutionary perspective. Copyright © 2017 Elsevier B.V. All rights reserved.

Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

PubMed

Beck, Emily A; Llopart, Ana

2015-11-25

Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.

Quantifying the rapid evolution of a nourishment project with video imagery

USGS Publications Warehouse

Elko, N.A.; Holman, R.A.; Gelfenbaum, G.

2005-01-01

Spatially and temporally high-resolution video imagery was combined with traditional surveyed beach profiles to investigate the evolution of a rapidly eroding beach nourishment project. Upham Beach is a 0.6-km beach located downdrift of a structured inlet on the west coast of Florida. The beach was stabilized in seaward advanced position during the 1960s and has been nourished every 4-5 years since 1975. During the 1996 nourishment project, 193,000 m 3 of sediment advanced the shoreline as much as 175 m. Video images were collected concurrent with traditional surveys during the 1996 nourishment project to test video imaging as a nourishment monitoring technique. Video imagery illustrated morphologic changes that were unapparent in survey data. Increased storminess during the second (El Nin??o) winter after the 1996 project resulted in increased erosion rates of 0.4 m/d (135.0 m/y) as compared with 0.2 m/d (69.4 m/y) during the first winter. The measured half-life, the time at which 50% of the nourished material remains, of the nourishment project was 0.94 years. A simple analytical equation indicates reasonable agreement with the measured values, suggesting that project evolution follows a predictable pattern of exponential decay. Long-shore planform equilibration does not occur on Upham Beach, rather sediment diffuses downdrift until 100% of the nourished material erodes. The wide nourished beach erodes rapidly due to the lack of sediment bypassing from the north and the stabilized headland at Upham Beach that is exposed to wave energy.

Rapidity evolution of Wilson lines at the next-to-leading order

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balitsky, Ian; Chirilli, Giovanni

2013-12-01

At high energies particles move very fast so the proper degrees of freedom for the fast gluons moving along the straight lines are Wilson-line operators - infinite gauge factors ordered along the line. In the framework of operator expansion in Wilson lines the energy dependence of the amplitudes is determined by the rapidity evolution of Wilson lines. We present the next-to-leading order hierarchy of the evolution equations for Wilson-line operators.

Archaeological data reveal slow rates of evolution during plant domestication.

PubMed

Purugganan, Michael D; Fuller, Dorian Q

2011-01-01

Domestication is an evolutionary process of species divergence in which morphological and physiological changes result from the cultivation/tending of plant or animal species by a mutualistic partner, most prominently humans. Darwin used domestication as an analogy to evolution by natural selection although there is strong debate on whether this process of species evolution by human association is an appropriate model for evolutionary study. There is a presumption that selection under domestication is strong and most models assume rapid evolution of cultivated species. Using archaeological data for 11 species from 60 archaeological sites, we measure rates of evolution in two plant domestication traits--nonshattering and grain/seed size increase. Contrary to previous assumptions, we find the rates of phenotypic evolution during domestication are slow, and significantly lower or comparable to those observed among wild species subjected to natural selection. Our study indicates that the magnitudes of the rates of evolution during the domestication process, including the strength of selection, may be similar to those measured for wild species. This suggests that domestication may be driven by unconscious selection pressures similar to that observed for natural selection, and the study of the domestication process may indeed prove to be a valid model for the study of evolutionary change. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

The Rapid Evolution of the Exciting Star of the Stingray Nebula

NASA Technical Reports Server (NTRS)

Reindl, N.; Rauch, T.; Parthasarathy, M.; Werner, K.; Kruk, J.W.; Hamann, W. R.; Sander, A.; Todt, H.

2014-01-01

Context: SAO244567, the exciting star of the Stingray nebula, is rapidly evolving. Previous analyses suggested that it has heated up from an effective temperature of about 21 kK in 1971 to over 50 kK in the 1990s. Canonical post-asymptotic giant branch evolution suggests a relatively high mass while previous analyses indicate a low-mass star. Aims: A comprehensive model-atmosphere analysis of UV and optical spectra taken during 1988-2006 should reveal the detailed temporal evolution of its atmospheric parameters and provide explanations for the unusually fast evolution. Methods: Fitting line profiles from static and expanding non-LTE model atmospheres to the observed spectra allowed us to study the temporal change of effective temperature, surface gravity, mass-loss rate, and terminal wind velocity. In addition, we determined the chemical composition of the atmosphere. Results: We find that the central star has steadily increased its effective temperature from 38 kK in 1988 to a peak value of 60 kK in 2002. During the same time, the star was contracting, as concluded from an increase in surface gravity from log g = 4.8 to 6.0 and a drop in luminosity. Simultaneously, the mass-loss rate declined from log(M/M (solar mass) yr (exp -1)) = -9.0 to -11.6 and the terminal wind velocity increased from v (infinity) = 1800 km s (exp -1) to 2800 km s (exp -1). Since around 2002, the star stopped heating and has cooled down again to 55 kK by 2006. It has a largely solar surface composition with the exception of slightly subsolar carbon, phosphorus, and sulfur. The results are discussed by considering different evolutionary scenarios. Conclusions: The position of SAO244567 in the log T (sub eff) -log g plane places the star in the region of sdO stars. By comparison with stellar-evolution calculations, we confirm that SAO244567 must be a low-mass star (M < 0.55 solar mass). However, the slow evolution of the respective stellar evolutionary models is in strong contrast to the observed fast evolution and the young planetary nebula with a kinematical age of only about 1000 years. We speculate that the star could be a late He-shell flash object. Alternatively, it could be the outcome of close-binary evolution. Then SAO244567 would be a low-mass (0.354 solar mass) helium pre-white dwarf after the common-envelope phase, during which the planetary nebula was ejected.

Eco-evolution in size-structured ecosystems: simulation case study of rapid morphological changes in alewife.

PubMed

Kang, Jung Koo; Thibert-Plante, Xavier

2017-02-27

Over the last 300 years, interactions between alewives and zooplankton communities in several lakes in the U.S. have caused the alewives' morphology to transition rapidly from anadromous to landlocked. Lakes with landlocked alewives contain smaller-bodied zooplankton than those without alewives. Landlocked adult alewives display smaller body sizes, narrower gapes, smaller inter-gill-raker spacings, reach maturity at an earlier age, and are less fecund than anadromous alewives. Additionally, landlocked alewives consume pelagic prey exclusively throughout their lives whereas anadromous alewives make an ontogenetic transition from pelagic to littoral prey. These rapid, well-documented changes in the alewives' morphology provide important insights into the morphological evolution of fish. Predicting the morphological evolution of fish is crucial for fisheries and ecosystem management, but the involvement of multiple trophic interactions make predictions difficult. To obtain an improved understanding of rapid morphological change in fish, we developed an individual-based model that simulated rapid changes in the body size and gill-raker count of a fish species in a hypothetical, size-structured prey community. Model parameter values were based mainly on data from empirical studies on alewives. We adopted a functional trait approach; consequently, the model explicitly describes the relationships between prey body size, alewife body size, and alewife gill-raker count. We sought to answer two questions: (1) How does the impact of alewife populations on prey feed back to impact alewife size and gill raker number under several alternative scenarios? (2) Will the trajectory of the landlocked alewives' morphological evolution change after 150-300 years in freshwater? Over the first 250 years, the alewives' numbers of gill-rakers only increased when reductions in their body size substantially improved their ability to forage for small prey. Additionally, alewives' gill-raker counts increased more rapidly as the adverse effects of narrow gill-raker spacings on foraging for large prey were made less severe. For the first 150-250 years, alewives' growth decreased monotonically, and their gill-raker number increased monotonically. After the first 150-250 years, however, the alewives exhibited multiple evolutionary morphological trajectories in different trophic settings. In several of these settings, their evolutionary trajectories even reversed after the first 150-250 years. Alewives affected the abundance and morphology of their prey, which in turn changed the abundance and morphology of the alewives. Complex low-trophic-level interactions can alter the abundance and characteristics of alewives. This study suggests that the current morphology of recently (∼300 years)-landlocked alewives may not represent an evolutionarily stable state.

Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories.

PubMed

Avigdor, Bracha Erlanger; Cimino-Mathews, Ashley; DeMarzo, Angelo M; Hicks, Jessica L; Shin, James; Sukumar, Saraswati; Fetting, John; Argani, Pedram; Park, Ben H; Wheelan, Sarah J

2017-12-21

Heterogeneity within and among tumors in a metastatic cancer patient is a well-established phenomenon that may confound treatment and accurate prognosis. Here, we used whole-exome sequencing to survey metastatic breast cancer tumors from 5 patients in a rapid autopsy program to construct the origin and genetic development of metastases. Metastases were obtained from 5 breast cancer patients using a rapid autopsy protocol and subjected to whole-exome sequencing. Metastases were evaluated for sharing of somatic mutations, correlation of copy number variation and loss of heterozygosity, and genetic similarity scores. Pathological features of the patients' disease were assessed by immunohistochemical analyses. Our data support a monoclonal origin of metastasis in 3 cases, but in 2 cases, metastases arose from at least 2 distinct subclones in the primary tumor. In the latter 2 cases, the primary tumor presented with mixed histologic and pathologic features, suggesting early divergent evolution within the primary tumor with maintenance of metastatic capability in multiple lineages. We used genetic and histopathological evidence to demonstrate that metastases can be derived from a single or multiple independent clones within a primary tumor. This underscores the complexity of breast cancer clonal evolution and has implications for how best to determine and implement therapies for early- and late-stage disease.

Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories

PubMed Central

Avigdor, Bracha Erlanger; Cimino-Mathews, Ashley; DeMarzo, Angelo M.; Hicks, Jessica L.; Shin, James; Sukumar, Saraswati; Fetting, John; Argani, Pedram; Park, Ben H.; Wheelan, Sarah J.

2017-01-01

Heterogeneity within and among tumors in a metastatic cancer patient is a well-established phenomenon that may confound treatment and accurate prognosis. Here, we used whole-exome sequencing to survey metastatic breast cancer tumors from 5 patients in a rapid autopsy program to construct the origin and genetic development of metastases. Metastases were obtained from 5 breast cancer patients using a rapid autopsy protocol and subjected to whole-exome sequencing. Metastases were evaluated for sharing of somatic mutations, correlation of copy number variation and loss of heterozygosity, and genetic similarity scores. Pathological features of the patients’ disease were assessed by immunohistochemical analyses. Our data support a monoclonal origin of metastasis in 3 cases, but in 2 cases, metastases arose from at least 2 distinct subclones in the primary tumor. In the latter 2 cases, the primary tumor presented with mixed histologic and pathologic features, suggesting early divergent evolution within the primary tumor with maintenance of metastatic capability in multiple lineages. We used genetic and histopathological evidence to demonstrate that metastases can be derived from a single or multiple independent clones within a primary tumor. This underscores the complexity of breast cancer clonal evolution and has implications for how best to determine and implement therapies for early- and late-stage disease. PMID:29263308

Rapid evolution of cuticular hydrocarbons in a species radiation of acoustically diverse Hawaiian crickets (Gryllidae: trigonidiinae: Laupala).

PubMed

Mullen, Sean P; Mendelson, Tamra C; Schal, Coby; Shaw, Kerry L

2007-01-01

Understanding the origin and maintenance of barriers to gene exchange is a central goal of speciation research. Hawaiian swordtail crickets (genus Laupala) represent one of the most rapidly speciating animal groups yet identified. Extensive acoustic diversity, strong premating isolation, and female preference for conspecific acoustic signals in laboratory phonotaxis trials have strongly supported divergence in mate recognition as the driving force behind the explosive speciation seen in this system. However, recent work has shown that female preference for conspecific male calling song does not extend to mate choice at close range among these crickets, leading to the hypothesis that additional sexual signals are involved in mate recognition and premating isolation. Here we examine patterns of variation in cuticular lipids among several species of Laupala from Maui and the Big Island of Hawaii. Results demonstrate (1) a rapid and dramatic evolution of cuticular lipid composition among species in this genus, (2) significant differences among males and females in cuticular lipid composition, and (3) a significant reduction in the complexity of cuticular lipid profiles in species from the Big Island of Hawaii as compared to two outgroup species from Maui. These results suggest that behavioral barriers to gene exchange in Laupala may be composed of multiple mate recognition signals, a pattern common in other cricket species.

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.

PubMed

Lagator, Mato; Colegrave, Nick; Neve, Paul

2014-11-07

In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

The formation and build-up of the red-sequence over the past 9 Gyr in VIPERS

NASA Astrophysics Data System (ADS)

Fritz, Alexander; Abbas, U.; Adami, C.; Arnouts, S.; Bel, J.; Bolzonella, M.; Bottini, D.; Branchini, E.; Burden, A.; Cappi, A.; Coupon, J.; Cucciati, O.; Davidzon, I.; De Lucia, G.; de la Torre, S.; Di Porto, C.; Franzetti, P.; Fumana, M.; Garilli, B.; Granett, B. R.; Guzzo, L.; Ilbert, O.; Iovino, A.; Krywult, J.; Le Brun, V.; Le Fèvre, O.; Maccagni, D.; Małek, K.; Marchetti, A.; Marinoni, C.; Marulli, F.; McCracken, H. J.; Mellier, Y.; Moscardini, L.; Nichol, R. C.; Paioro, L.; Peacock, J. A.; Percival, W. J.; Polletta, M.; Pollo, A.; Scodeggio, M.; Tasca, L. A. M.; Tojeiro, R.; Vergani, D.; Zamorani, G.; Zanichelli, A.; VIPERS Team

2015-02-01

We present the Luminosity Function (LF) and Colour-Magnitude Relation (CMR) using ~45000 galaxies drawn from the VIMOS Public Extragalactic Redshift Survey (VIPERS). Using different selection criteria, we define several samples of early-type galaxies and explore their impact on the evolution of the red-sequence (RS) and the effects of dust. Our results suggest a rapid build-up of the RS within a short time scale. We find a rise in the number density of early-type galaxies and a strong evolution in LF and CMR. Massive galaxies exist already 9 Gyr ago and experience an efficient quenching of their star formation at z = 1, followed by a passive evolution with only limited merging activity. In contrast, low-mass galaxies indicate a different mass assembly history and cause a slow build-up of the CMR over cosmic time.

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

PubMed Central

Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

2014-01-01

Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. PMID:25523484

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.

PubMed

Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

2014-12-19

Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.

Detecting self-ion irradiation-induced void swelling in pure copper using transient grating spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dennett, C. A.; So, K. P.; Kushima, A.

Irradiation-induced void swelling remains a major challenge to nuclear reactor operation. Swelling may take years to initiate and often results in rapid material property degradation once started. Alloy development for advanced nuclear systems will require rapid characterization of the swelling breakaway dose in new alloys, yet this capability does not yet exist. In this paper, we demonstrate that transient grating spectroscopy (TGS) can detect void swelling in single crystal copper via changes in surface acoustic wave (SAW) velocity. Scanning transmission electron microscopy (STEM) links the TGS-observed changes with void swelling-induced microstructural evolution. Finally, these results are considered in the contextmore » of previous work to suggest that in situ TGS will be able to rapidly determine when new bulk materials begin void swelling, shortening alloy development and testing times.« less

Detecting self-ion irradiation-induced void swelling in pure copper using transient grating spectroscopy

DOE PAGES

Dennett, C. A.; So, K. P.; Kushima, A.; ...

2017-12-20

Irradiation-induced void swelling remains a major challenge to nuclear reactor operation. Swelling may take years to initiate and often results in rapid material property degradation once started. Alloy development for advanced nuclear systems will require rapid characterization of the swelling breakaway dose in new alloys, yet this capability does not yet exist. In this paper, we demonstrate that transient grating spectroscopy (TGS) can detect void swelling in single crystal copper via changes in surface acoustic wave (SAW) velocity. Scanning transmission electron microscopy (STEM) links the TGS-observed changes with void swelling-induced microstructural evolution. Finally, these results are considered in the contextmore » of previous work to suggest that in situ TGS will be able to rapidly determine when new bulk materials begin void swelling, shortening alloy development and testing times.« less

Observational signatures of neutron stars in low-mass X-ray binaries climbing a stability peak

NASA Astrophysics Data System (ADS)

Kantor, E. M.; Gusakov, M. E.; Chugunov, A. I.

2016-01-01

In the recent papers by Gusakov et al., a new scenario describing evolution of rapidly rotating neutron stars (NSs) in low-mass X-ray binaries was proposed. The scenario accounts for a resonant interaction of normal r-modes with superfluid inertial modes at some specific internal stellar temperatures (`resonance temperatures'). This interaction results in an enhanced damping of r-mode and appearance of the `stability peaks' in the temperature - spin frequency plane, which split the r-mode instability window in the vicinity of the resonance temperatures. The scenario suggests that the hot and rapidly rotating NSs spend most of their life climbing up these peaks and, in particular, are observed there at the moment. We analyse in detail possible observational signatures of this suggestion. In particular, we show that these objects may exhibit `anti-glitches' - sudden frequency jumps on a time-scale of hours-months.

Effects of shortened host life span on the evolution of parasite life history and virulence in a microbial host-parasite system

PubMed Central

Nidelet, Thibault; Koella, Jacob C; Kaltz, Oliver

2009-01-01

Background Ecological factors play an important role in the evolution of parasite exploitation strategies. A common prediction is that, as shorter host life span reduces future opportunities of transmission, parasites compensate with an evolutionary shift towards earlier transmission. They may grow more rapidly within the host, have a shorter latency time and, consequently, be more virulent. Thus, increased extrinsic (i.e., not caused by the parasite) host mortality leads to the evolution of more virulent parasites. To test these predictions, we performed a serial transfer experiment, using the protozoan Paramecium caudatum and its bacterial parasite Holospora undulata. We simulated variation in host life span by killing hosts after 11 (early killing) or 14 (late killing) days post inoculation; after killing, parasite transmission stages were collected and used for a new infection cycle. Results After 13 cycles (≈ 300 generations), parasites from the early-killing treatment were less infectious, but had shorter latency time and higher virulence than those from the late-killing treatment. Overall, shorter latency time was associated with higher parasite loads and thus presumably with more rapid within-host replication. Conclusion The analysis of the means of the two treatments is thus consistent with theory, and suggests that evolution is constrained by trade-offs between virulence, transmission and within-host growth. In contrast, we found little evidence for such trade-offs across parasite selection lines within treatments; thus, to some extent, these traits may evolve independently. This study illustrates how environmental variation (experienced by the host) can lead to the evolution of distinct parasite strategies. PMID:19320981

Rapid evolution of analog circuits configured on a field programmable transistor array

NASA Technical Reports Server (NTRS)

Stoica, A.; Ferguson, M. I.; Zebulum, R. S.; Keymeulen, D.; Duong, V.; Daud, T.

2002-01-01

The purpose of this paper is to illustrate evolution of analog circuits on a stand-alone board-level evolvable system (SABLES). SABLES is part of an effort to achieve integrated evolvable systems. SABLES provides autonomous, fast (tens to hundreds of seconds), on-chip circuit evolution involving about 100,000 circuit evaluations. Its main components are a JPL Field Programmable Transistor Array (FPTA) chip used as transistor-level reconfigurable hardware, and a TI DSP that implements the evolutionary algorithm controlling the FPTA reconfiguration. The paper details an example of evolution on SABLES and points out to certain transient and memory effects that affect the stability of solutions obtained reusing the same piece of hardware for rapid testing of individuals during evolution.

Rapid recent human evolution and the accumulation of balanced genetic polymorphisms.

PubMed

Wills, Christopher

2011-01-01

All evolutionary change can be traced to alterations in allele frequencies in populations over time. DNA sequencing on a massive scale now permits us to follow the genetic consequences as our species has diverged from our close relatives and as we have colonized different parts of the world and adapted to them. But it has been difficult to disentangle natural selection from many other factors that alter frequencies. These factors include mutation and intragenic reciprocal recombination, gene conversion, segregation distortion, random drift, and gene flow between populations (these last two are greatly influenced by splits and coalescences of populations over time). The first part of this review examines recent studies that have had some success in dissecting out the role of natural selection, especially in humans and Drosophila. Among many examples, these studies include those that have followed the rapid evolution of traits that may permit adaptation to high altitude in Tibetan and Andean populations. In some cases, directional selection has been so strong that it may have swept alleles close to fixation in the span of a few thousand years, a rapidity of change that is also sometimes encountered in other organisms. The second part of the review summarizes data showing that remarkably few alleles have been carried completely to fixation during our recent evolution. Some of the alleles that have not reached fixation may be approaching new internal equilibria, which would indicate polymorphisms that are maintained by balancing selection. Finally, the review briefly examines why genetic polymorphisms, particularly those that are maintained by negative frequency dependence, are likely to have played an important role in the evolution of our species. A method is suggested for measuring the contribution of these polymorphisms to our gene pool. Such polymorphisms may add to the ability of our species to adapt to our increasingly complex and challenging environment. © Mary Ann Liebert, Inc.

Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates.

PubMed

King, Benedict; Qiao, Tuo; Lee, Michael S Y; Zhu, Min; Long, John A

2017-07-01

The phylogeny of early gnathostomes provides an important framework for understanding one of the most significant evolutionary events, the origin and diversification of jawed vertebrates. A series of recent cladistic analyses have suggested that the placoderms, an extinct group of armoured fish, form a paraphyletic group basal to all other jawed vertebrates. We revised and expanded this morphological data set, most notably by sampling autapomorphies in a similar way to parsimony-informative traits, thus ensuring this data (unlike most existing morphological data sets) satisfied an important assumption of Bayesian tip-dated morphological clock approaches. We also found problems with characters supporting placoderm paraphyly, including character correlation and incorrect codings. Analysis of this data set reveals that paraphyly and monophyly of core placoderms (excluding maxillate forms) are essentially equally parsimonious. The two alternative topologies have different root positions for the jawed vertebrates but are otherwise similar. However, analysis using tip-dated clock methods reveals strong support for placoderm monophyly, due to this analysis favoring trees with more balanced rates of evolution. Furthermore, enforcing placoderm paraphyly results in higher levels and unusual patterns of rate heterogeneity among branches, similar to that generated from simulated trees reconstructed with incorrect root positions. These simulations also show that Bayesian tip-dated clock methods outperform parsimony when the outgroup is largely uninformative (e.g., due to inapplicable characters), as might be the case here. The analysis also reveals that gnathostomes underwent a rapid burst of evolution during the Silurian period which declined during the Early Devonian. This rapid evolution during a period with few articulated fossils might partly explain the difficulty in ascertaining the root position of jawed vertebrates. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Sublimation as a landform-shaping process on Pluto

NASA Astrophysics Data System (ADS)

Moore, Jeffrey M.; Howard, Alan D.; Umurhan, Orkan M.; White, Oliver L.; Schenk, Paul M.; Beyer, Ross A.; McKinnon, William B.; Spencer, John R.; Grundy, Will M.; Lauer, Tod R.; Nimmo, Francis; Young, Leslie A.; Stern, S. Alan; Weaver, Harold A.; Olkin, Cathy B.; Ennico, Kimberly; New Horizons Science Team

2017-05-01

Fields of pits, both large and small, in Tombaugh Regio (Sputnik Planitia, and the Pitted Uplands to the east), and along the scarp of Piri Rupes, are examples of landscapes on Pluto where we conclude that sublimation drives their formation and evolution. Our heuristic modeling closely mimics the form, spacing, and arrangement of a variety of Tombaugh Regio's pits. Pluto's sublimation modified landforms appear to require a significant role for (diffusive) mass wasting as suggested by our modeling. In our models, the temporal evolution of pitted surfaces is such that initially lots of time passes with little happening, then eventually, very rapid development of relief and rapid sublimation. Small pits on Sputnik Planitia are consistent with their formation in N2-dominated materials. As N2-ice readily flows, some other ``stiffer'' volatile ice may play a role in supporting the relief of sublimation degraded landforms that exhibit several hundred meters of relief. A strong candidate is CH4, which is spectroscopically observed to be associated with these features, but the current state of rheological knowledge for CH4 ice at Pluto conditions is insufficient for a firm assessment.

The role of habitat shift in the evolution of lizard morphology: evidence from tropical Tropidurus

PubMed Central

Vitt, Laurie J.; Caldwell, Janalee P.; Zani, Peter A.; Titus, Tom A.

1997-01-01

We compared morphology of two geographically close populations of the tropical lizard Tropidurus hispidus to test the hypothesis that habitat structure influences the evolution of morphology and ecology at the population level. T. hispidus isolated on a rock outcrop surrounded by tropical forest use rock crevices for refuge and appear dorsoventrally compressed compared with those in open savanna. A principal components analysis revealed that the populations were differentially distributed along an axis representing primarily three components of shape: body width, body height, and hind-leg length. Morphological divergence was supported by a principal components analysis of size-free morphological variables. Mitochondrial DNA sequences of ATPase 6 indicate that these populations are closely related relative to other T. hispidus, the rock outcrop morphology and ecology are derived within T. hispidus, and morphological and ecological divergence has occurred more rapidly than genetic divergence. This suggests that natural selection can rapidly adjust morphology and ecology in response to a recent history of exposure to habitats differing in structure, a result heretofore implied from comparative studies among lizard species. PMID:9108063

The role of habitat shift in the evolution of lizard morphology: evidence from tropical Tropidurus.

PubMed

Vitt, L J; Caldwell, J P; Zani, P A; Titus, T A

1997-04-15

We compared morphology of two geographically close populations of the tropical lizard Tropidurus hispidus to test the hypothesis that habitat structure influences the evolution of morphology and ecology at the population level. T. hispidus isolated on a rock outcrop surrounded by tropical forest use rock crevices for refuge and appear dorsoventrally compressed compared with those in open savanna. A principal components analysis revealed that the populations were differentially distributed along an axis representing primarily three components of shape: body width, body height, and hind-leg length. Morphological divergence was supported by a principal components analysis of size-free morphological variables. Mitochondrial DNA sequences of ATPase 6 indicate that these populations are closely related relative to other T. hispidus, the rock outcrop morphology and ecology are derived within T. hispidus, and morphological and ecological divergence has occurred more rapidly than genetic divergence. This suggests that natural selection can rapidly adjust morphology and ecology in response to a recent history of exposure to habitats differing in structure, a result heretofore implied from comparative studies among lizard species.

Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes

PubMed Central

Fischbach, Michael A.; Lai, Jonathan R.; Roche, Eric D.; Walsh, Christopher T.; Liu, David R.

2007-01-01

Nonribosomal peptides (NRPs) are produced by NRP synthetase (NRPS) enzymes that function as molecular assembly lines. The modular architecture of NRPSs suggests that a domain responsible for activating a building block could be replaced with a domain from a foreign NRPS to create a chimeric assembly line that produces a new variant of a natural NRP. However, such chimeric NRPS modules are often heavily impaired, impeding efforts to create novel NRP variants by swapping domains from different modules or organisms. Here we show that impaired chimeric NRPSs can be functionally restored by directed evolution. Using rounds of mutagenesis coupled with in vivo screens for NRP production, we rapidly isolated variants of two different chimeric NRPSs with ≈10-fold improvements in enzyme activity and product yield, including one that produces new derivatives of the potent NRP/polyketide antibiotic andrimid. Because functional restoration in these examples required only modest library sizes (103 to 104 clones) and three or fewer rounds of screening, our approach may be widely applicable even for NRPSs from genetically challenging hosts. PMID:17620609

Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation.

PubMed

Corl, Ammon; Davis, Alison R; Kuchta, Shawn R; Sinervo, Barry

2010-03-02

Polymorphism may play an important role in speciation because new species could originate from the distinctive morphs observed in polymorphic populations. However, much remains to be understood about the process by which morphs found new species. To detail the steps of this mode of speciation, we studied the geographic variation and evolutionary history of a throat color polymorphism that distinguishes the "rock-paper-scissors" mating strategies of the side-blotched lizard, Uta stansburiana. We found that the polymorphism is geographically widespread and has been maintained for millions of years. However, there are many populations with reduced numbers of throat color morphs. Phylogenetic reconstruction showed that the polymorphism is ancestral, but it has been independently lost eight times, often giving rise to morphologically distinct subspecies/species. Changes to the polymorphism likely involved selection because the allele for one particular male strategy, the "sneaker" morph, has been lost in all cases. Polymorphism loss was associated with accelerated evolution of male size, female size, and sexual dimorphism, which suggests that polymorphism loss can promote rapid divergence among populations and aid species formation.

NLO Hierarchy of Wilson Lines Evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balitsky, Ian

2015-03-01

The high-energy behavior of QCD amplitudes can be described in terms of the rapidity evolution of Wilson lines. I present the hierarchy of evolution equations for Wilson lines in the next-to-leading order.

Dynamic Nucleotide Mutation Gradients and Control Region Usage in Squamate Reptile Mitochondrial Genomes

PubMed Central

Castoe, T.A.; Gu, W.; de Koning, A.P.J.; Daza, J.M.; Jiang, Z.J.; Parkinson, C.L.; Pollock, D.D.

2010-01-01

Gradients of nucleotide bias and substitution rates occur in vertebrate mitochondrial genomes due to the asymmetric nature of the replication process. The evolution of these gradients has previously been studied in detail in primates, but not in other vertebrate groups. From the primate study, the strengths of these gradients are known to evolve in ways that can substantially alter the substitution process, but it is unclear how rapidly they evolve over evolutionary time or how different they may be in different lineages or groups of vertebrates. Given the importance of mitochondrial genomes in phylogenetics and molecular evolutionary research, a better understanding of how asymmetric mitochondrial substitution gradients evolve would contribute key insights into how this gradient evolution may mislead evolutionary inferences, and how it may also be incorporated into new evolutionary models. Most snake mitochondrial genomes have an additional interesting feature, 2 nearly identical control regions, which vary among different species in the extent that they are used as origins of replication. Given the expanded sampling of complete snake genomes currently available, together with 2 additional snakes sequenced in this study, we reexamined gradient strength and CR usage in alethinophidian snakes as well as several lizards that possess dual CRs. Our results suggest that nucleotide substitution gradients (and corresponding nucleotide bias) and CR usage is highly labile over the ∼200 m.y. of squamate evolution, and demonstrates greater overall variability than previously shown in primates. The evidence for the existence of such gradients, and their ability to evolve rapidly and converge among unrelated species suggests that gradient dynamics could easily mislead phylogenetic and molecular evolutionary inferences, and argues strongly that these dynamics should be incorporated into phylogenetic models. PMID:20215734

Evidence for rapid topographic evolution and crater degradation on Mercury from simple crater morphometry

NASA Astrophysics Data System (ADS)

Fassett, Caleb I.; Crowley, Malinda C.; Leight, Clarissa; Dyar, M. Darby; Minton, David A.; Hirabayashi, Masatoshi; Thomson, Bradley J.; Watters, Wesley A.

2017-06-01

Examining the topography of impact craters and their evolution with time is useful for assessing how fast planetary surfaces evolve. Here, new measurements of depth/diameter (d/D) ratios for 204 craters of 2.5 to 5 km in diameter superposed on Mercury's smooth plains are reported. The median d/D is 0.13, much lower than expected for newly formed simple craters ( 0.21). In comparison, lunar craters that postdate the maria are much less modified, and the median crater in the same size range has a d/D ratio that is nearly indistinguishable from the fresh value. This difference in crater degradation is remarkable given that Mercury's smooth plains and the lunar maria likely have ages that are comparable, if not identical. Applying a topographic diffusion model, these results imply that crater degradation is faster by a factor of approximately two on Mercury than on the Moon, suggesting more rapid landform evolution on Mercury at all scales.