Science.gov

Sample records for accelerated sequence evolution

  1. Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome

    PubMed Central

    Dong, Xinran; Wang, Xiao; Zhang, Feng; Tian, Weidong

    2016-01-01

    Accelerated evolution of regulatory sequence can alter the expression pattern of target genes, and cause phenotypic changes. In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ∼0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions, and their expression levels are positively selected in the human brain. Thus, these lines of evidences strongly suggest that accelerated evolution on regulatory sequences plays important role in the evolution of human-specific phenotypes. PMID:27401230

  2. Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome.

    PubMed

    Dong, Xinran; Wang, Xiao; Zhang, Feng; Tian, Weidong

    2016-10-01

    Accelerated evolution of regulatory sequence can alter the expression pattern of target genes, and cause phenotypic changes. In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ∼0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions, and their expression levels are positively selected in the human brain. Thus, these lines of evidences strongly suggest that accelerated evolution on regulatory sequences plays important role in the evolution of human-specific phenotypes.

  3. Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences.

    PubMed

    Triant, Deborah A; Dewoody, J Andrew

    2006-01-01

    Microtus is one of the most taxonomically diverse mammalian genera, including over 60 extant species. These rodents have evolved rapidly, as the genus originated less than 2 million years ago. If these numbers are taken at face value, then an average of 30 microtine speciation events have occurred every million years. One explanation for the rapid rate of cladogenesis in Microtus could be the karyotypic differentiation exhibited across the genus: diploid numbers range from 17 to 64. Despite the striking chromosomal variability within Microtus, phenotypic variation is unremarkable. To determine whether nucleotide substitution rates are also elevated in voles, we sequenced the entire mitochondrial DNA (mtDNA) genome of the Eurasian sibling vole (Microtus rossiaemeridionalis). We compared this genome to another previously sequenced vole mtDNA genome (Microtus kikuchii) and performed pairwise sequence comparisons with the mtDNA genomes of ten additional mammalian genera. We found that microtine mtDNA genomes are evolving more rapidly than any other mammalian lineage we sampled, as gauged by the rate of nucleotide substitution across the entire mtDNA genome as well as at each individual protein-coding gene. Additionally, we compared substitution rates within the cytochrome b gene to seven other rodent genera and found that Microtus mtDNA is evolving fastest. The root cause of accelerated evolution in Microtus remains uncertain, but merits further investigation.

  4. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes.

    PubMed

    Sloan, Daniel B; Triant, Deborah A; Wu, Martin; Taylor, Douglas R

    2014-03-01

    Many mitochondrial and plastid protein complexes contain subunits that are encoded in different genomes. In animals, nuclear-encoded mitochondrial proteins often exhibit rapid sequence evolution, which has been hypothesized to result from selection for mutations that compensate for changes in interacting subunits encoded in mutation-prone animal mitochondrial DNA. To test this hypothesis, we analyzed nuclear genes encoding cytosolic and organelle ribosomal proteins in flowering plants. The model angiosperm genus Arabidopsis exhibits low organelle mutation rates, typical of most plants. Nevertheless, we found that (nuclear-encoded) subunits of organelle ribosomes in Arabidopsis have higher amino acid sequence polymorphism and divergence than their counterparts in cytosolic ribosomes, suggesting that organelle ribosomes experience relaxed functional constraint. However, the observed difference between organelle and cytosolic ribosomes was smaller than in animals and could be partially attributed to rapid evolution in N-terminal organelle-targeting peptides that are not involved in ribosome function. To test the role of organelle mutation more directly, we used transcriptomic data from an angiosperm genus (Silene) with highly variable rates of organelle genome evolution. We found that Silene species with unusually fast-evolving mitochondrial and plastid DNA exhibited increased amino acid sequence divergence in ribosomal proteins targeted to the organelles but not in those that function in cytosolic ribosomes. Overall, these findings support the hypothesis that rapid organelle genome evolution has selected for compensatory mutations in nuclear-encoded proteins. We conclude that coevolution between interacting subunits encoded in different genomic compartments within the eukaryotic cell is an important determinant of variation in rates of protein sequence evolution.

  5. Accelerated Evolution of Conserved Noncoding Sequences in theHuman Genome

    SciTech Connect

    Prambhakar, Shyam; Noonan, James P.; Paabo, Svante; Rubin, EdwardM.

    2006-07-06

    Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detect"cryptic" functional elements, which are too weakly conserved amongmammals to distinguish from nonfunctional DNA. To address this problem,we explored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.

  6. Extinction events can accelerate evolution.

    PubMed

    Lehman, Joel; Miikkulainen, Risto

    2015-01-01

    Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term.

  7. Extinction Events Can Accelerate Evolution

    PubMed Central

    Lehman, Joel; Miikkulainen, Risto

    2015-01-01

    Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term. PMID:26266804

  8. Evolution of DNA sequencing.

    PubMed

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-03-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted in it. Detection of terminated sequences was done radiographically on Polyacrylamide Gel Electrophoresis (PAGE). Improvements that have evolved over time in original Sanger sequencing include replacement of radiography with fluorescence, use of separate fluorescent markers for each nucleotide, use of capillary electrophoresis instead of polyacrylamide gel electrophoresis and then introduction of capillary array electrophoresis. However, this technique suffered from few inherent limitations like decreased sensitivity for low level mutant alleles, complexities in analyzing highly polymorphic regions like Major Histocompatibility Complex (MHC) and high DNA concentrations required. Several Next Generation Sequencing (NGS) technologies have been introduced by Roche, Illumina and other commercial manufacturers that tend to overcome Sanger sequencing limitations and have been reviewed. Introduction of NGS in clinical research and medical diagnostics is expected to change entire diagnostic approach. These include study of cancer variants, detection of minimal residual disease, exome sequencing, detection of Single Nucleotide Polymorphisms (SNPs) and their disease association, epigenetic regulation of gene expression and sequencing of microorganisms genome.

  9. Mercury BLASTP: Accelerating Protein Sequence Alignment

    PubMed Central

    Jacob, Arpith; Lancaster, Joseph; Buhler, Jeremy; Harris, Brandon; Chamberlain, Roger D.

    2008-01-01

    Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we describe the architecture of the portions of the application that are accelerated in the FPGA, and we also describe the integration of these FPGA-accelerated portions with the existing BLASTP software. We have implemented Mercury BLASTP on a commodity workstation with two Xilinx Virtex-II 6000 FPGAs. We show that the new design runs 11-15 times faster than software BLASTP on a modern CPU while delivering close to 99% identical results. PMID:19492068

  10. Acceleration of convergence of vector sequences

    NASA Technical Reports Server (NTRS)

    Sidi, A.; Ford, W. F.; Smith, D. A.

    1983-01-01

    A general approach to the construction of convergence acceleration methods for vector sequence is proposed. Using this approach, one can generate some known methods, such as the minimal polynomial extrapolation, the reduced rank extrapolation, and the topological epsilon algorithm, and also some new ones. Some of the new methods are easier to implement than the known methods and are observed to have similar numerical properties. The convergence analysis of these new methods is carried out, and it is shown that they are especially suitable for accelerating the convergence of vector sequences that are obtained when one solves linear systems of equations iteratively. A stability analysis is also given, and numerical examples are provided. The convergence and stability properties of the topological epsilon algorithm are likewise given.

  11. Nucleotide sequence determines the accelerated rate of point mutations.

    PubMed

    Kini, R Manjunatha; Chinnasamy, Arunkumar

    2010-09-01

    Although the theory of evolution was put forth about 150 years ago our understanding of how molecules drive evolution remains poor. It is well-established that proteins evolve at different rates, essentially based on their functional role and three-dimensional structure. However, the highly variable rates of evolution of different proteins - especially the rapidly evolving ones - within a single organism are poorly understood. Using examples of genes for fast-evolving toxins and human hereditary diseases, we show for the first time that specific nucleotide sequences appear to determine point mutation rates. Based on mutation rates, we have classified triplets (not just codons) into stable, unstable and intermediate groups. Toxin genes contain a relatively higher percentage of unstable triplets in their exons compared to introns, whereas non-toxin genes contain a higher percentage of unstable triplets in their introns. Thus the distribution of stable and unstable triplets is correlated with and may explain the accelerated evolution of point mutations in toxins. Similarly, at the genomic level, lower organisms with genes that evolve faster contain a higher percentage of unstable triplets compared to higher organisms. These findings show that mutation rates of proteins, and hence of the organisms, are DNA sequence-dependent and thus provide a proximate mechanism of evolution at the molecular level. PMID:20362603

  12. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...

  13. Accelerated Evolution in the Death Galaxy

    NASA Astrophysics Data System (ADS)

    Austin, Robert; Tung, Chih-Kuan; Gong, Xiu-Quing; Lambert, Guillaume; Liao, David

    2010-03-01

    We recall 4 main guiding principles of evolution: 1) instability of defections, 2) stress induced non-random mutations, 3) genetic heterogeneity, and 4) fragmented populations. Our previous preliminary experiments have been relatively simple 1-D stress experiments. We are proceeding with 2-D experiments whose design is guided by these principles. Our new experiment we have dubbed the Death Galaxy because of it's use of these design principles. The ``galaxy'' name comes from the fact that the structure is designed as an interconnected array of micro-ecologies, these micro-ecologies are similar to the stars that comprise an astronomical galaxy, and provide the fragmented small populations. A gradient of the antibiotic Cipro is introduced across the galaxy, and we will present results which show how bacterial evolution resulting in resistance to Cipro is accelerated by the physics principles underlying the device.

  14. The evolution of nanopore sequencing

    PubMed Central

    Wang, Yue; Yang, Qiuping; Wang, Zhimin

    2014-01-01

    The “$1000 Genome” project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the “$1000 Genome” while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards. PMID:25610451

  15. REvolver: modeling sequence evolution under domain constraints.

    PubMed

    Koestler, Tina; von Haeseler, Arndt; Ebersberger, Ingo

    2012-09-01

    Simulating the change of protein sequences over time in a biologically realistic way is fundamental for a broad range of studies with a focus on evolution. It is, thus, problematic that typically simulators evolve individual sites of a sequence identically and independently. More realistic simulations are possible; however, they are often prohibited by limited knowledge concerning site-specific evolutionary constraints or functional dependencies between amino acids. As a consequence, a protein's functional and structural characteristics are rapidly lost in the course of simulated evolution. Here, we present REvolver (www.cibiv.at/software/revolver), a program that simulates protein sequence alteration such that evolutionarily stable sequence characteristics, like functional domains, are maintained. For this purpose, REvolver recruits profile hidden Markov models (pHMMs) for parameterizing site-specific models of sequence evolution in an automated fashion. pHMMs derived from alignments of homologous proteins or protein domains capture information regarding which sequence sites remained conserved over time and where in a sequence insertions or deletions are more likely to occur. Thus, they describe constraints on the evolutionary process acting on these sequences. To demonstrate the performance of REvolver as well as its applicability in large-scale simulation studies, we evolved the entire human proteome up to 1.5 expected substitutions per site. Simultaneously, we analyzed the preservation of Pfam and SMART domains in the simulated sequences over time. REvolver preserved 92% of the Pfam domains originally present in the human sequences. This value drops to 15% when traditional models of amino acid sequence evolution are used. Thus, REvolver represents a significant advance toward a realistic simulation of protein sequence evolution on a proteome-wide scale. Further, REvolver facilitates the simulation of a protein family with a user-defined domain architecture at

  16. Insights into hominid evolution from the gorilla genome sequence

    PubMed Central

    Scally, Aylwyn; Dutheil, Julien Y.; Hillier, LaDeana W.; Jordan, Greg E.; Goodhead, Ian; Herrero, Javier; Hobolth, Asger; Lappalainen, Tuuli; Mailund, Thomas; Marques-Bonet, Tomas; McCarthy, Shane; Montgomery, Stephen H.; Schwalie, Petra C.; Tang, Y. Amy; Ward, Michelle C.; Xue, Yali; Yngvadottir, Bryndis; Alkan, Can; Andersen, Lars N.; Ayub, Qasim; Ball, Edward V.; Beal, Kathryn; Bradley, Brenda J.; Chen, Yuan; Clee, Chris M.; Fitzgerald, Stephen; Graves, Tina A.; Gu, Yong; Heath, Paul; Heger, Andreas; Karakoc, Emre; Kolb-Kokocinski, Anja; Laird, Gavin K.; Lunter, Gerton; Meader, Stephen; Mort, Matthew; Mullikin, James C.; Munch, Kasper; O’Connor, Timothy D.; Phillips, Andrew D.; Prado-Martinez, Javier; Rogers, Anthony S.; Sajjadian, Saba; Schmidt, Dominic; Shaw, Katy; Simpson, Jared T.; Stenson, Peter D.; Turner, Daniel J.; Vigilant, Linda; Vilella, Albert J.; Whitener, Weldon; Zhu, Baoli; Cooper, David N.; de Jong, Pieter; Dermitzakis, Emmanouil T.; Eichler, Evan E.; Flicek, Paul; Goldman, Nick; Mundy, Nicholas I.; Ning, Zemin; Odom, Duncan T.; Ponting, Chris P.; Quail, Michael A.; Ryder, Oliver A.; Searle, Stephen M.; Warren, Wesley C.; Wilson, Richard K.; Schierup, Mikkel H.; Rogers, Jane; Tyler-Smith, Chris; Durbin, Richard

    2012-01-01

    Summary Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. PMID:22398555

  17. Randomness in Sequence Evolution Increases over Time.

    PubMed

    Wang, Guangyu; Sun, Shixiang; Zhang, Zhang

    2016-01-01

    The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution. PMID:27224236

  18. Randomness in Sequence Evolution Increases over Time

    PubMed Central

    Wang, Guangyu; Sun, Shixiang; Zhang, Zhang

    2016-01-01

    The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution. PMID:27224236

  19. DNA and RNA editing of retrotransposons accelerate mammalian genome evolution.

    PubMed

    Knisbacher, Binyamin A; Levanon, Erez Y

    2015-04-01

    Genome evolution is commonly viewed as a gradual process that is driven by random mutations that accumulate over time. However, DNA- and RNA-editing enzymes have been identified that can accelerate evolution by actively modifying the genomically encoded information. The apolipoprotein B mRNA editing enzymes, catalytic polypeptide-like (APOBECs) are potent restriction factors that can inhibit retroelements by cytosine-to-uridine editing of retroelement DNA after reverse transcription. In some cases, a retroelement may successfully integrate into the genome despite being hypermutated. Such events introduce unique sequences into the genome and are thus a source of genomic innovation. adenosine deaminases that act on RNA (ADARs) catalyze adenosine-to-inosine editing in double-stranded RNA, commonly formed by oppositely oriented retroelements. The RNA editing confers plasticity to the transcriptome by generating many transcript variants from a single genomic locus. If the editing produces a beneficial variant, the genome may maintain the locus that produces the RNA-edited transcript for its novel function. Here, we discuss how these two powerful editing mechanisms, which both target inserted retroelements, facilitate expedited genome evolution.

  20. Protein sequence comparison and protein evolution

    SciTech Connect

    Pearson, W.R.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  1. Accelerating Genome Sequencing 100X with FPGAs

    SciTech Connect

    Storaasli, Olaf O; Strenski, Dave

    2007-01-01

    The performance of two Cray XD1 systems with Virtex-II Pro 50 and Virtex-4 LX160 FPGAs was evaluated using the FASTA computational biology program for human genome (DNA and protein) sequence comparisons. FPGA speedups of 50X (Virtex-II Pro 50) and 100X (Virtex-4 LX160) over a 2.2 GHz Opteron were obtained. FPGA coding issues for human genome data are described.

  2. Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor

    PubMed Central

    Holloway, Alisha K.; Bruneau, Benoit G.; Sukonnik, Tatyana; Rubenstein, John L.; Pollard, Katherine S.

    2016-01-01

    Mammals have evolved remarkably different sensory, reproductive, metabolic, and skeletal systems. To explore the genetic basis for these differences, we developed a comparative genomics approach to scan whole-genome multiple sequence alignments to identify regions that evolved rapidly in an ancestral lineage but are conserved within extant species. This pattern suggests that ancestral changes in function were maintained in descendants. After applying this test to therian mammals, we identified 4,797 accelerated regions, many of which are noncoding and located near developmental transcription factors. We then used mouse transgenic reporter assays to test if noncoding accelerated regions are enhancers and to determine how therian-specific substitutions affect their activity in vivo. We discovered enhancers with expression specific to the therian version in brain regions involved in the hormonal control of milk ejection, uterine contractions, blood pressure, temperature, and visual processing. This work underscores the idea that changes in developmental gene expression are important for mammalian evolution, and it pinpoints candidate genes for unique aspects of mammalian biology. PMID:26715627

  3. Archaebacterial rhodopsin sequences: Implications for evolution

    NASA Technical Reports Server (NTRS)

    Lanyi, J. K.

    1991-01-01

    It was proposed over 10 years ago that the archaebacteria represent a separate kingdom which diverged very early from the eubacteria and eukaryotes. It follows that investigations of archaebacterial characteristics might reveal features of early evolution. So far, two genes, one for bacteriorhodopsin and another for halorhodopsin, both from Halobacterium halobium, have been sequenced. We cloned and sequenced the gene coding for the polypeptide of another one of these rhodopsins, a halorhodopsin in Natronobacterium pharaonis. Peptide sequencing of cyanogen bromide fragments, and immuno-reactions of the protein and synthetic peptides derived from the C-terminal gene sequence, confirmed that the open reading frame was the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences of this gene, as well as those of other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences were calculated. These indicate very considerable evolutionary distance between each pair of genes, even in the dame organism. In spite of this, three protein sequences show extensive similarities, indicating strong selective pressures.

  4. Accelerated FoxP2 evolution in echolocating bats.

    PubMed

    Li, Gang; Wang, Jinhong; Rossiter, Stephen J; Jones, Gareth; Zhang, Shuyi

    2007-01-01

    FOXP2 is a transcription factor implicated in the development and neural control of orofacial coordination, particularly with respect to vocalisation. Observations that orthologues show almost no variation across vertebrates yet differ by two amino acids between humans and chimpanzees have led to speculation that recent evolutionary changes might relate to the emergence of language. Echolocating bats face especially challenging sensorimotor demands, using vocal signals for orientation and often for prey capture. To determine whether mutations in the FoxP2 gene could be associated with echolocation, we sequenced FoxP2 from echolocating and non-echolocating bats as well as a range of other mammal species. We found that contrary to previous reports, FoxP2 is not highly conserved across all nonhuman mammals but is extremely diverse in echolocating bats. We detected divergent selection (a change in selective pressure) at FoxP2 between bats with contrasting sonar systems, suggesting the intriguing possibility of a role for FoxP2 in the evolution and development of echolocation. We speculate that observed accelerated evolution of FoxP2 in bats supports a previously proposed function in sensorimotor coordination.

  5. The evolution of high energy accelerators

    SciTech Connect

    Courant, E.D.

    1994-08-01

    Accelerators have been devised and built for two reasons: In the first place, by physicists who needed high energy particles in order to have a means to explore the interactions between particles that probe the fundamental elementary forces of nature. And conversely, sometimes accelerator builders produce new machines for higher energy than ever before just because it can be done, and then challenge potential users to make new discoveries with the new means at hand. These two approaches or motivations have gone hand in hand. This lecture traces how high energy particle accelerators have grown from tools used for esoteric small-scale experiments to the gigantic projects of today. So far all the really high-energy machines built and planned in the world--except the SLC--have been ring accelerators and storage rings using the strong-focusing method. But this method has not removed the energy limit, it has only pushed it higher. It would seem unlikely that one can go beyond the Large Hadron Collider (LHC)--but in fact a workshop was held in Sicily in November 1991, concerned with the question of extrapolating to 100 TeV. Other acceleration and beam-forming methods are now being discussed--collective fields, laser acceleration, wake-field accelerators etc., all aimed primarily at making linear colliders possible and more attractive than with present radiofrequency methods. So far it is not entirely clear which of these schemes will dominate particle physics in the future--maybe something that has not been thought of as yet.

  6. Adaptive radiation of venomous marine snail lineages and the accelerated evolution of venom peptide genes.

    PubMed

    Olivera, Baldomero M; Watkins, Maren; Bandyopadhyay, Pradip; Imperial, Julita S; de la Cotera, Edgar P Heimer; Aguilar, Manuel B; Vera, Estuardo López; Concepcion, Gisela P; Lluisma, Arturo

    2012-09-01

    An impressive biodiversity (>10,000 species) of marine snails (suborder Toxoglossa or superfamily Conoidea) have complex venoms, each containing approximately 100 biologically active, disulfide-rich peptides. In the genus Conus, the most intensively investigated toxoglossan lineage (∼500 species), a small set of venom gene superfamilies undergo rapid sequence hyperdiversification within their mature toxin regions. Each major lineage of Toxoglossa has its own distinct set of venom gene superfamilies. Two recently identified venom gene superfamilies are expressed in the large Turridae clade, but not in Conus. Thus, as major venomous molluscan clades expand, a small set of lineage-specific venom gene superfamilies undergo accelerated evolution. The juxtaposition of extremely conserved signal sequences with hypervariable mature peptide regions is unprecedented and raises the possibility that in these gene superfamilies, the signal sequences are conserved as a result of an essential role they play in enabling rapid sequence evolution of the region of the gene that encodes the active toxin.

  7. Evolution of magnetohydrodynamic waves and associated ultrarelativistic electron acceleration

    SciTech Connect

    Takeyama, Yosuke; Nakayama, Shun-ichi; Ohsawa, Yukiharu

    2011-09-15

    The evolution of magnetosonic shock waves and Alfven waves generated by a strong disturbance and electron acceleration occurring in these waves is studied with fully kinetic, relativistic, electromagnetic, particle simulations. If two plasmas collide, magnetic field lines are compressed near the initial boundary of the two, resulting in the formation of a strong-magnetic-field pulse, which reflects ions of the two plasmas in two opposite directions. These ion motions create forward and backward shock waves. Furthermore, large-amplitude Alfven waves are produced, with their propagation speeds much lower than the shock speeds. In the Alfven wave region, three types of ultrarelativistic electron acceleration are observed, which are analyzed in detail.

  8. Refuting the hypothesis that the acquisition of germ plasm accelerates animal evolution

    PubMed Central

    Whittle, Carrie A.; Extavour, Cassandra G.

    2016-01-01

    Primordial germ cells (PGCs) give rise to the germ line in animals. PGCs are specified during embryogenesis either by an ancestral mechanism of cell–cell signalling (induction) or by a derived mechanism of maternally provided germ plasm (preformation). Recently, a hypothesis was set forth purporting that germ plasm liberates selective constraint and accelerates an organism's protein sequence evolution, especially for genes from early developmental stages, thereby leading to animal species radiations; empirical validation has been claimed in vertebrates. Here we present findings from global rates of protein evolution in vertebrates and invertebrates refuting this hypothesis. Contrary to assertions of the hypothesis, we find no effect of preformation on protein sequence evolution, the evolutionary rates of early-stage developmental genes, or on species diversification. We conclude that the hypothesis is mechanistically implausible, and our multi-faceted analysis shows no empirical support for any of its predictions. PMID:27577604

  9. Refuting the hypothesis that the acquisition of germ plasm accelerates animal evolution.

    PubMed

    Whittle, Carrie A; Extavour, Cassandra G

    2016-01-01

    Primordial germ cells (PGCs) give rise to the germ line in animals. PGCs are specified during embryogenesis either by an ancestral mechanism of cell-cell signalling (induction) or by a derived mechanism of maternally provided germ plasm (preformation). Recently, a hypothesis was set forth purporting that germ plasm liberates selective constraint and accelerates an organism's protein sequence evolution, especially for genes from early developmental stages, thereby leading to animal species radiations; empirical validation has been claimed in vertebrates. Here we present findings from global rates of protein evolution in vertebrates and invertebrates refuting this hypothesis. Contrary to assertions of the hypothesis, we find no effect of preformation on protein sequence evolution, the evolutionary rates of early-stage developmental genes, or on species diversification. We conclude that the hypothesis is mechanistically implausible, and our multi-faceted analysis shows no empirical support for any of its predictions. PMID:27577604

  10. A taste of pineapple evolution through genome sequencing.

    PubMed

    Xu, Qing; Liu, Zhong-Jian

    2015-12-01

    The genome sequence assembly of the highly heterozygous Ananas comosus and its varieties is an impressive technical achievement. The sequence opens the door to a greater understanding of pineapple morphology and evolution. PMID:26620110

  11. A taste of pineapple evolution through genome sequencing.

    PubMed

    Xu, Qing; Liu, Zhong-Jian

    2015-12-01

    The genome sequence assembly of the highly heterozygous Ananas comosus and its varieties is an impressive technical achievement. The sequence opens the door to a greater understanding of pineapple morphology and evolution.

  12. Next-generation sequencing for understanding and accelerating crop domestication.

    PubMed

    Henry, Robert J

    2012-01-01

    Next generation Sequencing (NGS) provides a powerful tool for discovery of domestication genes in crop plants and their wild relatives. The accelerated domestication of new plant species as crops may be facilitated by this knowledge. Re-sequencing of domesticated genotypes can identify regions of low diversity associated with domestication. Species-specific data can be obtained from related wild species by whole-genome shot-gun sequencing. This sequence data can be used to design species specific polymerase chain reaction (PCR) primers. Sequencing of the products of PCR amplification of target genes can be used to explore genetic variation in large numbers of genes and gene families. Novel allelic variation in close or distant relatives can be characterized by NGS. Examples of recent applications of NGS to capture of genetic diversity for crop improvement include rice, sugarcane and Eucalypts. Populations of large numbers of individuals can be screened rapidly. NGS supports the rapid domestication of new plant species and the efficient identification and capture of novel genetic variation from related species.

  13. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

    PubMed Central

    Dugas, Diana V.; Hernandez, David; Koenen, Erik J.M.; Schwarz, Erika; Straub, Shannon; Hughes, Colin E.; Jansen, Robert K.; Nageswara-Rao, Madhugiri; Staats, Martijn; Trujillo, Joshua T.; Hajrah, Nahid H.; Alharbi, Njud S.; Al-Malki, Abdulrahman L.; Sabir, Jamal S. M.; Bailey, C. Donovan

    2015-01-01

    The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms. PMID:26592928

  14. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP.

    PubMed

    Dugas, Diana V; Hernandez, David; Koenen, Erik J M; Schwarz, Erika; Straub, Shannon; Hughes, Colin E; Jansen, Robert K; Nageswara-Rao, Madhugiri; Staats, Martijn; Trujillo, Joshua T; Hajrah, Nahid H; Alharbi, Njud S; Al-Malki, Abdulrahman L; Sabir, Jamal S M; Bailey, C Donovan

    2015-11-23

    The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.

  15. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP.

    PubMed

    Dugas, Diana V; Hernandez, David; Koenen, Erik J M; Schwarz, Erika; Straub, Shannon; Hughes, Colin E; Jansen, Robert K; Nageswara-Rao, Madhugiri; Staats, Martijn; Trujillo, Joshua T; Hajrah, Nahid H; Alharbi, Njud S; Al-Malki, Abdulrahman L; Sabir, Jamal S M; Bailey, C Donovan

    2015-01-01

    The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms. PMID:26592928

  16. Rapid evolution accelerates plant population spread in fragmented experimental landscapes.

    PubMed

    Williams, Jennifer L; Kendall, Bruce E; Levine, Jonathan M

    2016-07-29

    Predicting the speed of biological invasions and native species migrations requires an understanding of the ecological and evolutionary dynamics of spreading populations. Theory predicts that evolution can accelerate species' spread velocity, but how landscape patchiness--an important control over traits under selection--influences this process is unknown. We manipulated the response to selection in populations of a model plant species spreading through replicated experimental landscapes of varying patchiness. After six generations of change, evolving populations spread 11% farther than nonevolving populations in continuously favorable landscapes and 200% farther in the most fragmented landscapes. The greater effect of evolution on spread in patchier landscapes was consistent with the evolution of dispersal and competitive ability. Accounting for evolutionary change may be critical when predicting the velocity of range expansions. PMID:27471303

  17. Rapid evolution accelerates plant population spread in fragmented experimental landscapes.

    PubMed

    Williams, Jennifer L; Kendall, Bruce E; Levine, Jonathan M

    2016-07-29

    Predicting the speed of biological invasions and native species migrations requires an understanding of the ecological and evolutionary dynamics of spreading populations. Theory predicts that evolution can accelerate species' spread velocity, but how landscape patchiness--an important control over traits under selection--influences this process is unknown. We manipulated the response to selection in populations of a model plant species spreading through replicated experimental landscapes of varying patchiness. After six generations of change, evolving populations spread 11% farther than nonevolving populations in continuously favorable landscapes and 200% farther in the most fragmented landscapes. The greater effect of evolution on spread in patchier landscapes was consistent with the evolution of dispersal and competitive ability. Accounting for evolutionary change may be critical when predicting the velocity of range expansions.

  18. Mutational Pathway Determines Whether Drug Gradients Accelerate Evolution of Drug-Resistant Cells

    NASA Astrophysics Data System (ADS)

    Greulich, Philip; Waclaw, Bartłomiej; Allen, Rosalind J.

    2012-08-01

    Drug gradients are believed to play an important role in the evolution of bacteria resistant to antibiotics and tumors resistant to anticancer drugs. We use a statistical physics model to study the evolution of a population of malignant cells exposed to drug gradients, where drug resistance emerges via a mutational pathway involving multiple mutations. We show that a nonuniform drug distribution has the potential to accelerate the emergence of resistance when the mutational pathway involves a long sequence of mutants with increasing resistance, but if the pathway is short or crosses a fitness valley, the evolution of resistance may actually be slowed down by drug gradients. These predictions can be verified experimentally, and may help to improve strategies for combating the emergence of resistance.

  19. The Turning and Evolution of the Recent Acceleration Universe

    NASA Astrophysics Data System (ADS)

    Zhang, Tianxi; Tan, A.

    2007-05-01

    The turning point and evolution characteristics of the universe are investigated through solving the Friedmann equation with a non-zero cosmological constant. Choosing the present-time Hubble constant, the radius of the present universe , and the density parameter in matter as three key parameters, we obtain the density parameter in dark energy, the cosmological constant, the mass of the universe, the turning point redshif, the age of the present universe, and the time-dependent expansion rate, velocity, radius, and acceleration parameter of the universe. It is shown that the turing point redshift is soly dependent of the density parameters in matter and dark energy. For the flat universe, it turned from past deceleration to recent acceleration when its size was 1/2 to 2/3 of the present size if the density parameter in matter is between 0.2 and 0.4. The expansion rate is very large at initial and decreases with time to approach the Hubble constant. The expansion velocity can be over the light speed in the early period, which decreases to the minimum at the turning point and then increases with time to approach the ratio of the present radius to the Hubble radius times the square root of the density parameter in dark energy. The solution of the time-dependent radius increases with time. The present time depends on the three key parameters. The universe with a larger present radius, smaller Hubble constant, or smaller density parameter in dark energy is elder. The universe with greater density parameter in dark energy accelerates faster recently. The open and closed universes can also be accelerated recently. The turning points and evolution characteristics among different types of the universe and different sets of key parameters are compared. This presentation will show the details, supported by NASA grant (NNG04GD59G).

  20. Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover

    PubMed Central

    Farkas, Zoltán; Horvath, Peter; Bódi, Zoltán; Daraba, Andreea; Szamecz, Béla; Gut, Ivo; Bayes, Mónica; Santos, Manuel A. S.; Pál, Csaba

    2015-01-01

    Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome–mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that

  1. Singular accelerated evolution in massive F (R ) bigravity

    NASA Astrophysics Data System (ADS)

    Nojiri, S.; Odintsov, S. D.; Oikonomou, V. K.

    2015-12-01

    The possibility to have singular accelerated evolution in the context of F (R ) bimetric gravity is investigated. Particularly, we study two singular models of cosmological evolution, one of which is a singular modified version of the Starobinsky R2 inflation model. As we demonstrate, for both models in some cases, the slow-roll parameters become singular at the Type IV singularity, a fact that we interpret as a dynamical instability of the theory under study. This dynamical instability may be an indicator of a graceful exit from inflation, and we thoroughly discuss this scenario and the interpretation of the singular slow-roll parameters. Furthermore, it is demonstrated that for some versions of F (R ) bigravity, singular inflation is realized in a consistent way so that inflationary indices are compatible with Planck data. Moreover, we study the late-time behavior of the two singular models, and we show that the unified description of early- and late-time acceleration can be achieved in the context of bimetric F (R ) gravity.

  2. Accelerated evolution of constraint elements for hematophagic adaptation in mosquitoes.

    PubMed

    Wang, Ming-Shan; Adeola, Adeniyi C; Li, Yan; Zhang, Ya-Ping; Wu, Dong-Dong

    2015-11-18

    Comparative genomics is a powerful approach that comprehensively interprets the genome. Herein, we performed whole genome comparative analysis of 16 Diptera genomes, including four mosquitoes and 12 Drosophilae. We found more than 540 000 constraint elements (CEs) in the Diptera genome, with the majority found in the intergenic, coding and intronic regions. Accelerated elements (AEs) identified in mosquitoes were mostly in the protein-coding regions (>93%), which differs from vertebrates in genomic distribution. Some genes functionally enriched in blood digestion, body temperature regulation and insecticide resistance showed rapid evolution not only in the lineage of the recent common ancestor of mosquitoes (RCAM), but also in some mosquito lineages. This may be associated with lineage-specific traits and/or adaptations in comparison with other insects. Our findings revealed that although universally fast evolution acted on biological systems in RCAM, such as hematophagy, same adaptations also appear to have occurred through distinct degrees of evolution in different mosquito species, enabling them to be successful blood feeders in different environments.

  3. Further Examples of Evolution by Gene Duplication Revealed through DNA Sequence Comparisons

    PubMed Central

    Ohta, T.

    1994-01-01

    To test the theory that evolution by gene duplication occurs as a result of positive Darwinian selection that accompanies the acceleration of mutant substitutions, DNA sequences of recent duplication were analyzed by estimating the numbers of synonymous and nonsynonymous substitutions. For the troponin C family, at the period of differentiation of the fast and slow isoforms, amino acid substitutions were shown to have been accelerated relative to synonymous substitutions. Comparison of the first exon of α-actin genes revealed that amino acid substitutions were accelerated when the smooth muscle, skeletal and cardiac isoforms differentiated. Analysis of members of the heat shock protein 70 gene family of mammals indicates that heat shock responsive genes including duplicated copies are evolving rapidly, contrary to the cognitive genes which have been evolutionarily conservative. For the α(1)-antitrypsin reactive center, the acceleration of amino acid substitution has been found for gene pairs of recent duplication. PMID:7896112

  4. Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae.

    PubMed

    Guisinger, Mary M; Chumley, Timothy W; Kuehl, Jennifer V; Boore, Jeffrey L; Jansen, Robert K

    2010-02-01

    Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes.

  5. Sexual selection accelerates signal evolution during speciation in birds

    PubMed Central

    Seddon, Nathalie; Botero, Carlos A.; Tobias, Joseph A.; Dunn, Peter O.; MacGregor, Hannah E. A.; Rubenstein, Dustin R.; Uy, J. Albert C.; Weir, Jason T.; Whittingham, Linda A.; Safran, Rebecca J.

    2013-01-01

    Sexual selection is proposed to be an important driver of diversification in animal systems, yet previous tests of this hypothesis have produced mixed results and the mechanisms involved remain unclear. Here, we use a novel phylogenetic approach to assess the influence of sexual selection on patterns of evolutionary change during 84 recent speciation events across 23 passerine bird families. We show that elevated levels of sexual selection are associated with more rapid phenotypic divergence between related lineages, and that this effect is restricted to male plumage traits proposed to function in mate choice and species recognition. Conversely, we found no evidence that sexual selection promoted divergence in female plumage traits, or in male traits related to foraging and locomotion. These results provide strong evidence that female choice and male–male competition are dominant mechanisms driving divergence during speciation in birds, potentially linking sexual selection to the accelerated evolution of pre-mating reproductive isolation. PMID:23864596

  6. Sexual selection accelerates signal evolution during speciation in birds.

    PubMed

    Seddon, Nathalie; Botero, Carlos A; Tobias, Joseph A; Dunn, Peter O; Macgregor, Hannah E A; Rubenstein, Dustin R; Uy, J Albert C; Weir, Jason T; Whittingham, Linda A; Safran, Rebecca J

    2013-09-01

    Sexual selection is proposed to be an important driver of diversification in animal systems, yet previous tests of this hypothesis have produced mixed results and the mechanisms involved remain unclear. Here, we use a novel phylogenetic approach to assess the influence of sexual selection on patterns of evolutionary change during 84 recent speciation events across 23 passerine bird families. We show that elevated levels of sexual selection are associated with more rapid phenotypic divergence between related lineages, and that this effect is restricted to male plumage traits proposed to function in mate choice and species recognition. Conversely, we found no evidence that sexual selection promoted divergence in female plumage traits, or in male traits related to foraging and locomotion. These results provide strong evidence that female choice and male-male competition are dominant mechanisms driving divergence during speciation in birds, potentially linking sexual selection to the accelerated evolution of pre-mating reproductive isolation.

  7. Evolution Analysis of Simple Sequence Repeats in Plant Genome.

    PubMed

    Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

    2015-01-01

    Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1-3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.

  8. Evolution Analysis of Simple Sequence Repeats in Plant Genome

    PubMed Central

    Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

    2015-01-01

    Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution. PMID:26630570

  9. Evolution of cis-regulatory sequence and function in Diptera.

    PubMed

    Wittkopp, P J

    2006-09-01

    Cis-regulatory sequences direct patterns of gene expression essential for development and physiology. Evolutionary changes in these sequences contribute to phenotypic divergence. Despite their importance, cis-regulatory regions remain one of the most enigmatic features of the genome. Patterns of sequence evolution can be used to identify cis-regulatory elements, but the power of this approach depends upon the relationship between sequence and function. Comparative studies of gene regulation among Diptera reveal that divergent sequences can underlie conserved expression, and that expression differences can evolve despite largely similar sequences. This complex structure-function relationship is the primary impediment for computational identification and interpretation of cis-regulatory sequences. Biochemical characterization and in vivo assays of cis-regulatory sequences on a genomic-scale will relieve this barrier.

  10. Sedimentary sequence evolution in a Foredeep basin: Eastern Venezuela

    SciTech Connect

    Bejarano, C.; Funes, D.; Sarzalho, S.; Audemard, F.; Flores, G.

    1996-08-01

    Well log-seismic sequence stratigraphy analysis in the Eastern Venezuela Foreland Basin leads to study of the evolution of sedimentary sequences onto the Cretaceous-Paleocene passive margin. This basin comprises two different foredeep sub-basins: The Guarico subbasin to the west, older, and the Maturin sub-basin to the east, younger. A foredeep switching between these two sub-basins is observed at 12.5 m.y. Seismic interpretation and well log sections across the study area show sedimentary sequences with transgressive sands and coastal onlaps to the east-southeast for the Guarico sub-basin, as well as truncations below the switching sequence (12.5 m.y.), and the Maturin sub-basin shows apparent coastal onlaps to the west-northwest, as well as a marine onlap (deeper water) in the west, where it starts to establish. Sequence stratigraphy analysis of these sequences with well logs allowed the study of the evolution of stratigraphic section from Paleocene to middle Miocene (68.0-12.0 m.y.). On the basis of well log patterns, the sequences were divided in regressive-transgressive-regressive sedimentary cycles caused by changes in relative sea level. Facies distributions were analyzed and the sequences were divided into simple sequences or sub- sequences of a greater frequencies than third order depositional sequences.

  11. Post-main-sequence planetary system evolution.

    PubMed

    Veras, Dimitri

    2016-02-01

    The fates of planetary systems provide unassailable insights into their formation and represent rich cross-disciplinary dynamical laboratories. Mounting observations of post-main-sequence planetary systems necessitate a complementary level of theoretical scrutiny. Here, I review the diverse dynamical processes which affect planets, asteroids, comets and pebbles as their parent stars evolve into giant branch, white dwarf and neutron stars. This reference provides a foundation for the interpretation and modelling of currently known systems and upcoming discoveries. PMID:26998326

  12. Post-main-sequence planetary system evolution

    PubMed Central

    Veras, Dimitri

    2016-01-01

    The fates of planetary systems provide unassailable insights into their formation and represent rich cross-disciplinary dynamical laboratories. Mounting observations of post-main-sequence planetary systems necessitate a complementary level of theoretical scrutiny. Here, I review the diverse dynamical processes which affect planets, asteroids, comets and pebbles as their parent stars evolve into giant branch, white dwarf and neutron stars. This reference provides a foundation for the interpretation and modelling of currently known systems and upcoming discoveries. PMID:26998326

  13. Post-main-sequence planetary system evolution.

    PubMed

    Veras, Dimitri

    2016-02-01

    The fates of planetary systems provide unassailable insights into their formation and represent rich cross-disciplinary dynamical laboratories. Mounting observations of post-main-sequence planetary systems necessitate a complementary level of theoretical scrutiny. Here, I review the diverse dynamical processes which affect planets, asteroids, comets and pebbles as their parent stars evolve into giant branch, white dwarf and neutron stars. This reference provides a foundation for the interpretation and modelling of currently known systems and upcoming discoveries.

  14. Sequence dependent hole evolution in DNA.

    PubMed

    Lakhno, V D

    2004-06-01

    The paper examines thedynamical behavior of a radical cation(G(+*)) generated in adouble stranded DNA for differentoligonucleotide sequences. The resonancehole tunneling through an oligonucleotidesequence is studied by the method ofnumerical integration of self-consistentquantum-mechanical equations. The holemotion is considered quantum mechanicallyand nucleotide base oscillations aretreated classically. The results obtaineddemonstrate a strong dependence of chargetransfer on the type of nucleotidesequence. The rates of the hole transferare calculated for different nucleotidesequences and compared with experimentaldata on the transfer from (G(+*))to a GGG unit.

  15. Integrating Sequence Evolution into Probabilistic Orthology Analysis.

    PubMed

    Ullah, Ikram; Sjöstrand, Joel; Andersson, Peter; Sennblad, Bengt; Lagergren, Jens

    2015-11-01

    Orthology analysis, that is, finding out whether a pair of homologous genes are orthologs - stemming from a speciation - or paralogs - stemming from a gene duplication - is of central importance in computational biology, genome annotation, and phylogenetic inference. In particular, an orthologous relationship makes functional equivalence of the two genes highly likely. A major approach to orthology analysis is to reconcile a gene tree to the corresponding species tree, (most commonly performed using the most parsimonious reconciliation, MPR). However, most such phylogenetic orthology methods infer the gene tree without considering the constraints implied by the species tree and, perhaps even more importantly, only allow the gene sequences to influence the orthology analysis through the a priori reconstructed gene tree. We propose a sound, comprehensive Bayesian Markov chain Monte Carlo-based method, DLRSOrthology, to compute orthology probabilities. It efficiently sums over the possible gene trees and jointly takes into account the current gene tree, all possible reconciliations to the species tree, and the, typically strong, signal conveyed by the sequences. We compare our method with PrIME-GEM, a probabilistic orthology approach built on a probabilistic duplication-loss model, and MrBayesMPR, a probabilistic orthology approach that is based on conventional Bayesian inference coupled with MPR. We find that DLRSOrthology outperforms these competing approaches on synthetic data as well as on biological data sets and is robust to incomplete taxon sampling artifacts. PMID:26130236

  16. Estimating evolution of temporal sequence changes: a practical approach to inferring ancestral developmental sequences and sequence heterochrony.

    PubMed

    Harrison, Luke B; Larsson, Hans C E

    2008-06-01

    Developmental biology often yields data in a temporal context. Temporal data in phylogenetic systematics has important uses in the field of evolutionary developmental biology and, in general, comparative biology. The evolution of temporal sequences, specifically developmental sequences, has proven difficult to examine due to the highly variable temporal progression of development. Issues concerning the analysis of temporal sequences and problems with current methods of analysis are discussed. We present here an algorithm to infer ancestral temporal sequences, quantify sequence heterochronies, and estimate pseudoreplicate consensus support for sequence changes using Parsimov-based genetic inference [PGi]. Real temporal developmental sequence data sets are used to compare PGi with currently used approaches, and PGi is shown to be the most efficient, accurate, and practical method to examine biological data and infer ancestral states on a phylogeny. The method is also expandable to address further issues in developmental evolution, namely modularity. PMID:18570033

  17. MODELING THE RED SEQUENCE: HIERARCHICAL GROWTH YET SLOW LUMINOSITY EVOLUTION

    SciTech Connect

    Skelton, Rosalind E.; Bell, Eric F.; Somerville, Rachel S.

    2012-07-01

    We explore the effects of mergers on the evolution of massive early-type galaxies by modeling the evolution of their stellar populations in a hierarchical context. We investigate how a realistic red sequence population set up by z {approx} 1 evolves under different assumptions for the merger and star formation histories, comparing changes in color, luminosity, and mass. The purely passive fading of existing red sequence galaxies, with no further mergers or star formation, results in dramatic changes at the bright end of the luminosity function and color-magnitude relation. Without mergers there is too much evolution in luminosity at a fixed space density compared to observations. The change in color and magnitude at a fixed mass resembles that of a passively evolving population that formed relatively recently, at z {approx} 2. Mergers among the red sequence population ('dry mergers') occurring after z = 1 build up mass, counteracting the fading of the existing stellar populations to give smaller changes in both color and luminosity for massive galaxies. By allowing some galaxies to migrate from the blue cloud onto the red sequence after z = 1 through gas-rich mergers, younger stellar populations are added to the red sequence. This manifestation of the progenitor bias increases the scatter in age and results in even smaller changes in color and luminosity between z = 1 and z = 0 at a fixed mass. The resultant evolution appears much slower, resembling the passive evolution of a population that formed at high redshift (z {approx} 3-5), and is in closer agreement with observations. We conclude that measurements of the luminosity and color evolution alone are not sufficient to distinguish between the purely passive evolution of an old population and cosmologically motivated hierarchical growth, although these scenarios have very different implications for the mass growth of early-type galaxies over the last half of cosmic history.

  18. Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence.

    PubMed

    Gysbers, Rachel; Tram, Kha; Gu, Jimmy; Li, Yingfu

    2015-01-01

    The mechanism by which enzymes arose from both abiotic and biological worlds remains an unsolved natural mystery. We postulate that an enzyme can emerge from any sequence of any functional polymer under permissive evolutionary conditions. To support this premise, we have arbitrarily chosen a 50-nucleotide DNA fragment encoding for the Bos taurus (cattle) albumin mRNA and subjected it to test-tube evolution to derive a catalytic DNA (DNAzyme) with RNA-cleavage activity. After only a few weeks, a DNAzyme with significant catalytic activity has surfaced. Sequence comparison reveals that seven nucleotides are responsible for the conversion of the noncatalytic sequence into the enzyme. Deep sequencing analysis of DNA pools along the evolution trajectory has identified individual mutations as the progressive drivers of the molecular evolution. Our findings demonstrate that an enzyme can indeed arise from a sequence of a functional polymer via permissive molecular evolution, a mechanism that may have been exploited by nature for the creation of the enormous repertoire of enzymes in the biological world today. PMID:26091540

  19. Evolution of Protein-binding DNA Sequences through Competitive Binding

    NASA Astrophysics Data System (ADS)

    Peng, Weiqun; Gerland, Ulrich; Hwa, Terence; Levine, Herbert

    2002-03-01

    The dynamics of in vitro DNA evolution controlled via competitive binding of DNA sequences to proteins has been explored in a recent serial transfer experiment footnote B. Dubertret, S.Liu, Q. Ouyang, A. Libchaber, Phys. Rev. Lett. 86, 6022 (2001).. Motivated by the experiment, we investigate a continuum model for this evolution process in various parameter regimes. We establish a self-consistent mean-field evolution equation, determine its dynamical properties and finite population size corrections. In addition, we discuss the experimental implications of our results.

  20. Marsupial Genome Sequences: Providing Insight into Evolution and Disease

    PubMed Central

    Deakin, Janine E.

    2012-01-01

    Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences. PMID:24278712

  1. New method to study DNA sequences: the languages of evolution.

    PubMed

    Spinelli, Gino; Mayer-Foulkes, David

    2008-04-01

    Recently, several authors have reported statistical evidence for deterministic dynamics in the flux of genetic information, suggesting that evolution involves the emergence and maintenance of a fractal landscape in DNA chains. Here we examine the idea that motif repetition lies at the origin of these statistical properties of DNA. To analyse repetition patterns we apply a modification of the BDS statistic, devised to analyze complex economic dynamics and adapted here to DNA sequence analysis. This provides a new method to detect structured signals in genetic information. We compare naturally occurring DNA sequences along the evolutionary tree with randomly generated sequences and also with simulated sequences with repetition motifs. For easier understanding, we also define a new statistic for a DNA sequence that constitutes a specific fingerprint. The new methods are applied to exon and intron DNA sequences, finding specific statistical differences. Moreover, by analysing DNA sequences of different species from Bacteria to Man, we explore the evolution of these linguistic DNA features along the evolutionary tree. The results are consistent with the idea that all the flux of DNA information need not be random, but may be structured along the evolutionary tree. The implications for evolutionary theory are discussed.

  2. Determinants of the rate of protein sequence evolution

    PubMed Central

    Zhang, Jianzhi; Yang, Jian-Rong

    2015-01-01

    The rate and mechanism of protein sequence evolution have been central questions in evolutionary biology since the 1960s. Although the rate of protein sequence evolution depends primarily on the level of functional constraint, exactly what constitutes functional constraint has remained unclear. The increasing availability of genomic data has allowed for much needed empirical examinations on the nature of functional constraint. These studies found that the evolutionary rate of a protein is predominantly influenced by its expression level rather than functional importance. A combination of theoretical and empirical analyses have identified multiple mechanisms behind these observations and demonstrated a prominent role that selection against errors in molecular and cellular processes plays in protein evolution. PMID:26055156

  3. The genome sequence of taurine cattle: a window to ruminant biology and evolution.

    PubMed

    Elsik, Christine G; Tellam, Ross L; Worley, Kim C; Gibbs, Richard A; Muzny, Donna M; Weinstock, George M; Adelson, David L; Eichler, Evan E; Elnitski, Laura; Guigó, Roderic; Hamernik, Debora L; Kappes, Steve M; Lewin, Harris A; Lynn, David J; Nicholas, Frank W; Reymond, Alexandre; Rijnkels, Monique; Skow, Loren C; Zdobnov, Evgeny M; Schook, Lawrence; Womack, James; Alioto, Tyler; Antonarakis, Stylianos E; Astashyn, Alex; Chapple, Charles E; Chen, Hsiu-Chuan; Chrast, Jacqueline; Câmara, Francisco; Ermolaeva, Olga; Henrichsen, Charlotte N; Hlavina, Wratko; Kapustin, Yuri; Kiryutin, Boris; Kitts, Paul; Kokocinski, Felix; Landrum, Melissa; Maglott, Donna; Pruitt, Kim; Sapojnikov, Victor; Searle, Stephen M; Solovyev, Victor; Souvorov, Alexandre; Ucla, Catherine; Wyss, Carine; Anzola, Juan M; Gerlach, Daniel; Elhaik, Eran; Graur, Dan; Reese, Justin T; Edgar, Robert C; McEwan, John C; Payne, Gemma M; Raison, Joy M; Junier, Thomas; Kriventseva, Evgenia V; Eyras, Eduardo; Plass, Mireya; Donthu, Ravikiran; Larkin, Denis M; Reecy, James; Yang, Mary Q; Chen, Lin; Cheng, Ze; Chitko-McKown, Carol G; Liu, George E; Matukumalli, Lakshmi K; Song, Jiuzhou; Zhu, Bin; Bradley, Daniel G; Brinkman, Fiona S L; Lau, Lilian P L; Whiteside, Matthew D; Walker, Angela; Wheeler, Thomas T; Casey, Theresa; German, J Bruce; Lemay, Danielle G; Maqbool, Nauman J; Molenaar, Adrian J; Seo, Seongwon; Stothard, Paul; Baldwin, Cynthia L; Baxter, Rebecca; Brinkmeyer-Langford, Candice L; Brown, Wendy C; Childers, Christopher P; Connelley, Timothy; Ellis, Shirley A; Fritz, Krista; Glass, Elizabeth J; Herzig, Carolyn T A; Iivanainen, Antti; Lahmers, Kevin K; Bennett, Anna K; Dickens, C Michael; Gilbert, James G R; Hagen, Darren E; Salih, Hanni; Aerts, Jan; Caetano, Alexandre R; Dalrymple, Brian; Garcia, Jose Fernando; Gill, Clare A; Hiendleder, Stefan G; Memili, Erdogan; Spurlock, Diane; Williams, John L; Alexander, Lee; Brownstein, Michael J; Guan, Leluo; Holt, Robert A; Jones, Steven J M; Marra, Marco A; Moore, Richard; Moore, Stephen S; Roberts, Andy; Taniguchi, Masaaki; Waterman, Richard C; Chacko, Joseph; Chandrabose, Mimi M; Cree, Andy; Dao, Marvin Diep; Dinh, Huyen H; Gabisi, Ramatu Ayiesha; Hines, Sandra; Hume, Jennifer; Jhangiani, Shalini N; Joshi, Vandita; Kovar, Christie L; Lewis, Lora R; Liu, Yih-Shin; Lopez, John; Morgan, Margaret B; Nguyen, Ngoc Bich; Okwuonu, Geoffrey O; Ruiz, San Juana; Santibanez, Jireh; Wright, Rita A; Buhay, Christian; Ding, Yan; Dugan-Rocha, Shannon; Herdandez, Judith; Holder, Michael; Sabo, Aniko; Egan, Amy; Goodell, Jason; Wilczek-Boney, Katarzyna; Fowler, Gerald R; Hitchens, Matthew Edward; Lozado, Ryan J; Moen, Charles; Steffen, David; Warren, James T; Zhang, Jingkun; Chiu, Readman; Schein, Jacqueline E; Durbin, K James; Havlak, Paul; Jiang, Huaiyang; Liu, Yue; Qin, Xiang; Ren, Yanru; Shen, Yufeng; Song, Henry; Bell, Stephanie Nicole; Davis, Clay; Johnson, Angela Jolivet; Lee, Sandra; Nazareth, Lynne V; Patel, Bella Mayurkumar; Pu, Ling-Ling; Vattathil, Selina; Williams, Rex Lee; Curry, Stacey; Hamilton, Cerissa; Sodergren, Erica; Wheeler, David A; Barris, Wes; Bennett, Gary L; Eggen, André; Green, Ronnie D; Harhay, Gregory P; Hobbs, Matthew; Jann, Oliver; Keele, John W; Kent, Matthew P; Lien, Sigbjørn; McKay, Stephanie D; McWilliam, Sean; Ratnakumar, Abhirami; Schnabel, Robert D; Smith, Timothy; Snelling, Warren M; Sonstegard, Tad S; Stone, Roger T; Sugimoto, Yoshikazu; Takasuga, Akiko; Taylor, Jeremy F; Van Tassell, Curtis P; Macneil, Michael D; Abatepaulo, Antonio R R; Abbey, Colette A; Ahola, Virpi; Almeida, Iassudara G; Amadio, Ariel F; Anatriello, Elen; Bahadue, Suria M; Biase, Fernando H; Boldt, Clayton R; Carroll, Jeffery A; Carvalho, Wanessa A; Cervelatti, Eliane P; Chacko, Elsa; Chapin, Jennifer E; Cheng, Ye; Choi, Jungwoo; Colley, Adam J; de Campos, Tatiana A; De Donato, Marcos; Santos, Isabel K F de Miranda; de Oliveira, Carlo J F; Deobald, Heather; Devinoy, Eve; Donohue, Kaitlin E; Dovc, Peter; Eberlein, Annett; Fitzsimmons, Carolyn J; Franzin, Alessandra M; Garcia, Gustavo R; Genini, Sem; Gladney, Cody J; Grant, Jason R; Greaser, Marion L; Green, Jonathan A; Hadsell, Darryl L; Hakimov, Hatam A; Halgren, Rob; Harrow, Jennifer L; Hart, Elizabeth A; Hastings, Nicola; Hernandez, Marta; Hu, Zhi-Liang; Ingham, Aaron; Iso-Touru, Terhi; Jamis, Catherine; Jensen, Kirsty; Kapetis, Dimos; Kerr, Tovah; Khalil, Sari S; Khatib, Hasan; Kolbehdari, Davood; Kumar, Charu G; Kumar, Dinesh; Leach, Richard; Lee, Justin C-M; Li, Changxi; Logan, Krystin M; Malinverni, Roberto; Marques, Elisa; Martin, William F; Martins, Natalia F; Maruyama, Sandra R; Mazza, Raffaele; McLean, Kim L; Medrano, Juan F; Moreno, Barbara T; Moré, Daniela D; Muntean, Carl T; Nandakumar, Hari P; Nogueira, Marcelo F G; Olsaker, Ingrid; Pant, Sameer D; Panzitta, Francesca; Pastor, Rosemeire C P; Poli, Mario A; Poslusny, Nathan; Rachagani, Satyanarayana; Ranganathan, Shoba; Razpet, Andrej; Riggs, Penny K; Rincon, Gonzalo; Rodriguez-Osorio, Nelida; Rodriguez-Zas, Sandra L; Romero, Natasha E; Rosenwald, Anne; Sando, Lillian; Schmutz, Sheila M; Shen, Libing; Sherman, Laura; Southey, Bruce R; Lutzow, Ylva Strandberg; Sweedler, Jonathan V; Tammen, Imke; Telugu, Bhanu Prakash V L; Urbanski, Jennifer M; Utsunomiya, Yuri T; Verschoor, Chris P; Waardenberg, Ashley J; Wang, Zhiquan; Ward, Robert; Weikard, Rosemarie; Welsh, Thomas H; White, Stephen N; Wilming, Laurens G; Wunderlich, Kris R; Yang, Jianqi; Zhao, Feng-Qi

    2009-04-24

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

  4. Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

    PubMed

    Parker-Katiraee, Layla; Carson, Andrew R; Yamada, Takahiro; Arnaud, Philippe; Feil, Robert; Abu-Amero, Sayeda N; Moore, Gudrun E; Kaneda, Masahiro; Perry, George H; Stone, Anne C; Lee, Charles; Meguro-Horike, Makiko; Sasaki, Hiroyuki; Kobayashi, Keiko; Nakabayashi, Kazuhiko; Scherer, Stephen W

    2007-05-01

    Imprinted genes are expressed in a parent-of-origin manner and are located in clusters throughout the genome. Aberrations in the expression of imprinted genes on human Chromosome 7 have been suggested to play a role in the etiologies of Russell-Silver Syndrome and autism. We describe the imprinting of KLF14, an intronless member of the Krüppel-like family of transcription factors located at Chromosome 7q32. We show that it has monoallelic maternal expression in all embryonic and extra-embryonic tissues studied, in both human and mouse. We examine epigenetic modifications in the KLF14 CpG island in both species and find this region to be hypomethylated. In addition, we perform chromatin immunoprecipitation and find that the murine Klf14 CpG island lacks allele-specific histone modifications. Despite the absence of these defining features, our analysis of Klf14 in offspring from DNA methyltransferase 3a conditional knockout mice reveals that the gene's expression is dependent upon a maternally methylated region. Due to the intronless nature of Klf14 and its homology to Klf16, we suggest that the gene is an ancient retrotransposed copy of Klf16. By sequence analysis of numerous species, we place the timing of this event after the divergence of Marsupialia, yet prior to the divergence of the Xenarthra superclade. We identify a large number of sequence variants in KLF14 and, using several measures of diversity, we determine that there is greater variability in the human lineage with a significantly increased number of nonsynonymous changes, suggesting human-specific accelerated evolution. Thus, KLF14 may be the first example of an imprinted transcript undergoing accelerated evolution in the human lineage. PMID:17480121

  5. Evolution of gene sequence in response to chromosomal location.

    PubMed

    Díaz-Castillo, Carlos; Golic, Kent G

    2007-09-01

    Evolutionary forces acting on the repetitive DNA of heterochromatin are not constrained by the same considerations that apply to protein-coding genes. Consequently, such sequences are subject to rapid evolutionary change. By examining the Troponin C gene family of Drosophila melanogaster, which has euchromatic and heterochromatic members, we find that protein-coding genes also evolve in response to their chromosomal location. The heterochromatic members of the family show a reduced CG content and increased variation in DNA sequence. We show that the CG reduction applies broadly to the protein-coding sequences of genes located at the heterochromatin:euchromatin interface, with a very strong correlation between CG content and the distance from centric heterochromatin. We also observe a similar trend in the transition from telomeric heterochromatin to euchromatin. We propose that the methylation of DNA is one of the forces driving this sequence evolution.

  6. Turbulence Evolution and Shock Acceleration of Solar Energetic Particles

    NASA Technical Reports Server (NTRS)

    Chee, Ng K.

    2007-01-01

    We model the effects of self-excitation/damping and shock transmission of Alfven waves on solar-energetic-particle (SEP) acceleration at a coronal-mass-ejection (CME) driven parallel shock. SEP-excited outward upstream waves speedily bootstrap acceleration. Shock transmission further raises the SEP-excited wave intensities at high wavenumbers but lowers them at low wavenumbers through wavenumber shift. Downstream, SEP excitation of inward waves and damping of outward waves tend to slow acceleration. Nevertheless, > 2000 km/s parallel shocks at approx. 3.5 solar radii can accelerate SEPs to 100 MeV in < 5 minutes.

  7. Nonlinear Modeling of the Aids Virus Genetic Sequence Evolution

    NASA Astrophysics Data System (ADS)

    Cocho, G.; Gelover-Santiago, A.; Martinez-Mekler, G.; Rodin, A.

    A network of coupled maps is introduced to model the evolution of the genetic sequence of the HIV1 AIDS virus. Within a space of RNA chemical composition, short range interactions correspond to mutations. Ecological constraints generate long range couplings. The resulting equations are of a reaction-diffusion type. Quasi-species with an error threshold emerge from the model dynamics. Predictions relating chemical composition regularity properties with the variability of the HIV RNA sequence agree with a statistical analysis from gene data banks. The model suggests a clue for an alternative therapeutical treatment.

  8. The pig X and Y Chromosomes: structure, sequence, and evolution.

    PubMed

    Skinner, Benjamin M; Sargent, Carole A; Churcher, Carol; Hunt, Toby; Herrero, Javier; Loveland, Jane E; Dunn, Matt; Louzada, Sandra; Fu, Beiyuan; Chow, William; Gilbert, James; Austin-Guest, Siobhan; Beal, Kathryn; Carvalho-Silva, Denise; Cheng, William; Gordon, Daria; Grafham, Darren; Hardy, Matt; Harley, Jo; Hauser, Heidi; Howden, Philip; Howe, Kerstin; Lachani, Kim; Ellis, Peter J I; Kelly, Daniel; Kerry, Giselle; Kerwin, James; Ng, Bee Ling; Threadgold, Glen; Wileman, Thomas; Wood, Jonathan M D; Yang, Fengtang; Harrow, Jen; Affara, Nabeel A; Tyler-Smith, Chris

    2016-01-01

    We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

  9. The pig X and Y Chromosomes: structure, sequence, and evolution

    PubMed Central

    Skinner, Benjamin M.; Sargent, Carole A.; Churcher, Carol; Hunt, Toby; Herrero, Javier; Loveland, Jane E.; Dunn, Matt; Louzada, Sandra; Fu, Beiyuan; Chow, William; Gilbert, James; Austin-Guest, Siobhan; Beal, Kathryn; Carvalho-Silva, Denise; Cheng, William; Gordon, Daria; Grafham, Darren; Hardy, Matt; Harley, Jo; Hauser, Heidi; Howden, Philip; Howe, Kerstin; Lachani, Kim; Ellis, Peter J.I.; Kelly, Daniel; Kerry, Giselle; Kerwin, James; Ng, Bee Ling; Threadgold, Glen; Wileman, Thomas; Wood, Jonathan M.D.; Yang, Fengtang; Harrow, Jen; Affara, Nabeel A.; Tyler-Smith, Chris

    2016-01-01

    We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes—both single copy and amplified—on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution. PMID:26560630

  10. Evolution of auroral acceleration region field-aligned current systems, plasma, and potentials observed by Cluster during substorms

    NASA Astrophysics Data System (ADS)

    Hull, A. J.; Chaston, C. C.; Fillingim, M. O.; Frey, H. U.; Goldstein, M. L.; Bonnell, J. W.; Mozer, F.

    2015-12-01

    The auroral acceleration region is an integral link in the chain of events that transpire during substorms, and the currents, plasma and electric fields undergo significant changes driven by complex dynamical processes deep in the magnetotail. The acceleration processes that occur therein accelerate and heat the plasma that ultimately leads to some of the most intense global substorm auroral displays. Though this region has garnered considerable attention, the temporal evolution of field-aligned current systems, associated acceleration processes, and resultant changes in the plasma constituents that occur during key stages of substorm development remain unclear. In this study we present a survey of Cluster traversals within and just above the auroral acceleration region (≤3 Re altitude) during substorms. Particular emphasis is on the spatial morphology and developmental sequence of auroral acceleration current systems, potentials and plasma constituents, with the aim of identifying controlling factors, and assessing auroral emmission consequences. Exploiting multi-point measurements from Cluster in combination with auroral imaging, we reveal the injection powered, Alfvenic nature of both the substorm onset and expansion of auroral particle acceleration. We show evidence that indicates substorm onsets are characterized by the gross-intensification and filamentation/striation of pre-existing large-scale current systems to smaller/dispersive scale Alfven waves. Such an evolutionary sequence has been suggested in theoretical models or single spacecraft data, but has not been demonstrated or characterized in multispacecraft observations until now. It is also shown how the Alfvenic variations over time may dissipate to form large-scale inverted-V structures characteristic of the quasi-static aurora. These findings suggest that, in addition to playing active roles in driving substorm aurora, inverted-V and Alfvenic acceleration processes are causally linked. Key

  11. Angular-momentum evolution in laser-plasma accelerators.

    PubMed

    Thaury, C; Guillaume, E; Corde, S; Lehe, R; Le Bouteiller, M; Ta Phuoc, K; Davoine, X; Rax, J M; Rousse, A; Malka, V

    2013-09-27

    The transverse properties of an electron beam are characterized by two quantities, the emittance which indicates the electron beam extent in the phase space and the angular momentum which allows for nonplanar electron trajectories. Whereas the emittance of electron beams produced in a laser-plasma accelerator has been measured in several experiments, their angular momentum has been scarcely studied. It was demonstrated that electrons in a laser-plasma accelerator carry some angular momentum, but its origin was not established. Here we identify one source of angular-momentum growth and we present experimental results showing that the angular-momentum content evolves during the acceleration.

  12. Rapid Evolution of Virus Sequences in Intrinsically Disordered Protein Regions

    PubMed Central

    Gitlin, Leonid; Hagai, Tzachi; LaBarbera, Anthony; Solovey, Mark; Andino, Raul

    2014-01-01

    Nodamura Virus (NoV) is a nodavirus originally isolated from insects that can replicate in a wide variety of hosts, including mammals. Because of their simplicity and ability to replicate in many diverse hosts, NoV, and the Nodaviridae in general, provide a unique window into the evolution of viruses and host-virus interactions. Here we show that the C-terminus of the viral polymerase exhibits extreme structural and evolutionary flexibility. Indeed, fewer than 10 positively charged residues from the 110 amino acid-long C-terminal region of protein A are required to support RNA1 replication. Strikingly, this region can be replaced by completely unrelated protein sequences, yet still produce a functional replicase. Structure predictions, as well as evolutionary and mutational analyses, indicate that the C-terminal region is structurally disordered and evolves faster than the rest of the viral proteome. Thus, the function of an intrinsically unstructured protein region can be independent of most of its primary sequence, conferring both functional robustness and sequence plasticity on the protein. Our results provide an experimental explanation for rapid evolution of unstructured regions, which enables an effective exploration of the sequence space, and likely function space, available to the virus. PMID:25502394

  13. Rapid evolution of virus sequences in intrinsically disordered protein regions.

    PubMed

    Gitlin, Leonid; Hagai, Tzachi; LaBarbera, Anthony; Solovey, Mark; Andino, Raul

    2014-12-01

    Nodamura Virus (NoV) is a nodavirus originally isolated from insects that can replicate in a wide variety of hosts, including mammals. Because of their simplicity and ability to replicate in many diverse hosts, NoV, and the Nodaviridae in general, provide a unique window into the evolution of viruses and host-virus interactions. Here we show that the C-terminus of the viral polymerase exhibits extreme structural and evolutionary flexibility. Indeed, fewer than 10 positively charged residues from the 110 amino acid-long C-terminal region of protein A are required to support RNA1 replication. Strikingly, this region can be replaced by completely unrelated protein sequences, yet still produce a functional replicase. Structure predictions, as well as evolutionary and mutational analyses, indicate that the C-terminal region is structurally disordered and evolves faster than the rest of the viral proteome. Thus, the function of an intrinsically unstructured protein region can be independent of most of its primary sequence, conferring both functional robustness and sequence plasticity on the protein. Our results provide an experimental explanation for rapid evolution of unstructured regions, which enables an effective exploration of the sequence space, and likely function space, available to the virus. PMID:25502394

  14. Myostatin rapid sequence evolution in ruminants predates domestication.

    PubMed

    Tellgren, Asa; Berglund, Ann-Charlotte; Savolainen, Peter; Janis, Christine M; Liberles, David A

    2004-12-01

    Myostatin (GDF-8) is a negative regulator of skeletal muscle development. This gene has previously been implicated in the double muscling phenotype in mice and cattle. A systematic analysis of myostatin sequence evolution in ruminants was performed in a phylogenetic context. The myostatin coding sequence was determined from duiker (Sylvicapra grimmia caffra), eland (Taurotragus derbianus), gaur (Bos gaurus), ibex (Capra ibex), impala (Aepyceros melampus rednilis), pronghorn (Antilocapra americana), and tahr (Hemitragus jemlahicus). Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (Ka/Ks) indicates that positive selection may have been operating on this gene during the time of divergence of Bovinae and Antilopinae, starting from approximately 23 million years ago, a period that appears to account for most of the sequence difference between myostatin in these groups. These periods of positive selective pressure on myostatin may correlate with changes in skeletal muscle mass during the same period. PMID:15522803

  15. The evolution of horizontal-branch stars - Theoretical sequences

    NASA Technical Reports Server (NTRS)

    Lee, Young-Wook; Demarque, Pierre

    1990-01-01

    A new grid of standard (i.e., solar CNO/Fe, no core rotation, and including semiconvection) horizontal-branch evolutionary sequences are presented which extend the grid of Sweigart both by including the final phase of core helium exhaustion and by using a finer grid of compositions. These sequences were constructed specifically for the studies of the Sandage period-shift effect and the second parameter phenomenon among the Galactic globular clusters. The numerical results for the observable characteristics of the sequences are tabulated which can be directly used to synthesize the observed horizontal-branch distributions. The present computations suggest that the observed difference in period change of RR Lyrae stars in the globular clusters M3 and M15 could be attributed, at least in the mean, to stellar evolution.

  16. Molecular evolution of herpesviruses: genomic and protein sequence comparisons.

    PubMed Central

    Karlin, S; Mocarski, E S; Schachtel, G A

    1994-01-01

    Phylogenetic reconstruction of herpesvirus evolution is generally founded on amino acid sequence comparisons of specific proteins. These are relevant to the evolution of the specific gene (or set of genes), but the resulting phylogeny may vary depending on the particular sequence chosen for analysis (or comparison). In the first part of this report, we compare 13 herpesvirus genomes by using a new multidimensional methodology based on distance measures and partial orderings of dinucleotide relative abundances. The sequences were analyzed with respect to (i) genomic compositional extremes; (ii) total distances within and between genomes; (iii) partial orderings among genomes relative to a set of sequence standards; (iv) concordance correlations of genome distances; and (v) consistency with the alpha-, beta-, gammaherpesvirus classification. Distance assessments within individual herpesvirus genomes show each to be quite homogeneous relative to the comparisons between genomes. The gammaherpesviruses, Epstein-Barr virus (EBV), herpesvirus saimiri, and bovine herpesvirus 4 are both diverse and separate from other herpesvirus classes, whereas alpha- and betaherpesviruses overlap. The analysis revealed that the most central genome (closest to a consensus herpesvirus genome and most individual herpesvirus sequences of different classes) is that of human herpesvirus 6, suggesting that this genome is closest to a progenitor herpesvirus. The shorter DNA distances among alphaherpesviruses supports the hypothesis that the alpha class is of relatively recent ancestry. In our collection, equine herpesvirus 1 (EHV1) stands out as the most central alphaherpesvirus, suggesting it may approximate an ancestral alphaherpesvirus. Among all herpesviruses, the EBV genome is closest to human sequences. In the DNA partial orderings, the chicken sequence collection is invariably as close as or closer to all herpesvirus sequences than the human sequence collection is, which may imply that

  17. Biophysical and structural considerations for protein sequence evolution

    PubMed Central

    2011-01-01

    Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. PMID:22171550

  18. Sequence heterogeneity accelerates protein search for targets on DNA

    NASA Astrophysics Data System (ADS)

    Shvets, Alexey A.; Kolomeisky, Anatoly B.

    2015-12-01

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

  19. Sequence heterogeneity accelerates protein search for targets on DNA

    SciTech Connect

    Shvets, Alexey A.; Kolomeisky, Anatoly B.

    2015-12-28

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

  20. Accelerating Genome Sequencing 100-1000X with FPGAs

    SciTech Connect

    Storaasli, Olaf O

    2008-01-01

    The performance of FPGAs on Cray XD1 and SGI/RASC systems (with Virtex-II Pro 50 and Virtex-4 LX160 FPGAs) was evaluated for human genome sequencing using FASTA1 and BLAST2, respectively. Scalable speedups of 100X for a Virtex-4 FPGA (and exceeding 1000X for multiple FPGAs) over a 2.2 GHz Opteron were achieved. Similar FPGA speedups were achieved using BLAST on a SGI/RASC system at Oak Ridge National Laboratory.

  1. Sequence Heterogeneity Accelerates Protein Search for Targets on DNA

    NASA Astrophysics Data System (ADS)

    Shvets, Alexey; Kolomeisky, Anatoly

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry and heterogeneity of a genome. The work was supported by the Welch Foundation (Grant C-1559), by the NSF (Grant CHE-1360979), and by the Center for Theoretical Biological Physics sponsored by the NSF (Grant PHY-1427654).

  2. Co-evolution of metabolism and protein sequences.

    PubMed

    Schütte, Moritz; Klitgord, Niels; Segrè, Daniel; Ebenhöh, Oliver

    2010-01-01

    The set of chemicals producible and usable by metabolic pathways must have evolved in parallel with the enzymes that catalyze them. One implication of this common historical path should be a correspondence between the innovation steps that gradually added new metabolic reactions to the biosphere-level biochemical toolkit, and the gradual sequence changes that must have slowly shaped the corresponding enzyme structures. However, global signatures of a long-term co-evolution have not been identified. Here we search for such signatures by computing correlations between inter-reaction distances on a metabolic network, and sequence distances of the corresponding enzyme proteins. We perform our calculations using the set of all known metabolic reactions, available from the KEGG database. Reaction-reaction distance on the metabolic network is computed as the length of the shortest path on a projection of the metabolic network, in which nodes are reactions and edges indicate whether two reactions share a common metabolite, after removal of cofactors. Estimating the distance between enzyme sequences in a meaningful way requires some special care: for each enzyme commission (EC) number, we select from KEGG a consensus set of protein sequences using the cluster of orthologous groups of proteins (COG) database. We define the evolutionary distance between protein sequences as an asymmetric transition probability between two enzymes, derived from the corresponding pair-wise BLAST scores. By comparing the distances between sequences to the minimal distances on the metabolic reaction graph, we find a small but statistically significant correlation between the two measures. This suggests that the evolutionary walk in enzyme sequence space has locally mirrored, to some extent, the gradual expansion of metabolism. PMID:20238426

  3. DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

    PubMed Central

    Page, Justin T.; Liechty, Zach S.; Clemons, Kimberly; Hulse-Kemp, Amanda M.; Van Deynze, Allen; Stelly, David M.

    2016-01-01

    Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the AT- and DT-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars. PMID:27168520

  4. Evolution of Pre-Main Sequence Accretion Disks

    NASA Technical Reports Server (NTRS)

    Hartmann, Lee W.

    2003-01-01

    The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

  5. Sequence diversity and evolution of antimicrobial peptides in invertebrates.

    PubMed

    Tassanakajon, Anchalee; Somboonwiwat, Kunlaya; Amparyup, Piti

    2015-02-01

    Antimicrobial peptides (AMPs) are evolutionarily ancient molecules that act as the key components in the invertebrate innate immunity against invading pathogens. Several AMPs have been identified and characterized in invertebrates, and found to display considerable diversity in their amino acid sequence, structure and biological activity. AMP genes appear to have rapidly evolved, which might have arisen from the co-evolutionary arms race between host and pathogens, and enabled organisms to survive in different microbial environments. Here, the sequence diversity of invertebrate AMPs (defensins, cecropins, crustins and anti-lipopolysaccharide factors) are presented to provide a better understanding of the evolution pattern of these peptides that play a major role in host defense mechanisms.

  6. Accelerated evolution of morph-biased genes in pea aphids.

    PubMed

    Purandare, Swapna R; Bickel, Ryan D; Jaquiery, Julie; Rispe, Claude; Brisson, Jennifer A

    2014-08-01

    Phenotypic plasticity, the production of alternative phenotypes (or morphs) from the same genotype due to environmental factors, results in some genes being expressed in a morph-biased manner. Theoretically, these morph-biased genes experience relaxed selection, the consequence of which is the buildup of slightly deleterious mutations at these genes. Over time, this is expected to result in increased protein divergence at these genes between species and a signature of relaxed purifying selection within species. Here we test these theoretical expectations using morph-biased genes in the pea aphid, a species that produces multiple morphs via polyphenism. We find that morph-biased genes exhibit faster rates of evolution (in terms of dN/dS) relative to unbiased genes and that divergence generally increases with increasing morph bias. Further, genes with expression biased toward rarer morphs (sexual females and males) show faster rates of evolution than genes expressed in the more common morph (asexual females), demonstrating that the amount of time a gene spends being expressed in a morph is associated with its rate of evolution. And finally, we show that genes expressed in the rarer morphs experience decreased purifying selection relative to unbiased genes, suggesting that it is a relaxation of purifying selection that contributes to their faster rates of evolution. Our results provide an important empirical look at the impact of phenotypic plasticity on gene evolution.

  7. Stellar evolution from the zero-age main sequence

    NASA Technical Reports Server (NTRS)

    Mengel, J. G.; Demarque, P.; Sweigart, A. V.; Gross, P. G.

    1979-01-01

    A consistent set of 247 evolutionary sequences extending from the ZAMS to the red-giant branch is presented for Y from 0.10 to 0.40, Z from 0.00001 to 0.10, and masses of 0.55 to 6.90 solar masses. Each sequence is started from a homogeneous ZAMS model, and almost all are evolved to the base of the red-giant branch. It is shown that: (1) the relative position of the main sequence can be determined as a function of composition; (2) theoretical luminosity functions can be derived from the relative evolutionary time scales; (3) a dip in luminosity sometimes occurs at the base of the red-giant branch and is most pronounced at larger Z values; (4) metal-poor stars evolve farther up along the main sequence before turning off toward the red-giant branch; and (5) the onset of helium burning halts the evolution across the Hertzsprung gap for the most massive and most metal-poor models, so that the star remains blue during its phase of core-helium burning.

  8. DNA sequence evolution with neighbor-dependent mutation.

    PubMed

    Arndt, Peter F; Burge, Christopher B; Hwa, Terence

    2003-01-01

    We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of models is developed by adopting well-known methods of nonlinear dynamics. Results are presented for the CpG-methylation-deamination process, which dominates point substitutions in vertebrates. The dinucleotide frequencies generated by the model (using empirically obtained mutation rates) match the overall pattern observed in noncoding DNA. A web-based tool has been constructed to compute single- and dinucleotide frequencies for arbitrary neighbor-dependent mutation rates. Also provided is the backward procedure to infer the mutation rates using maximum likelihood analysis given the observed single- and dinucleotide frequencies. Reasonable estimates of the mutation rates can be obtained very efficiently, using generic noncoding DNA sequences as input, after masking out long homonucleotide subsequences. Our method is much more convenient and versatile to use than the traditional method of deducing mutation rates by counting mutation events in carefully chosen sequences. More generally, our approach provides a more realistic but still tractable description of noncoding genomic DNA and may be used as a null model for various sequence analysis applications.

  9. Niche divergence accelerates evolution in Asian endemic Procapra gazelles

    PubMed Central

    Hu, Junhua; Jiang, Zhigang; Chen, Jing; Qiao, Huijie

    2015-01-01

    Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system–based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species’ bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification. PMID:25951051

  10. Niche divergence accelerates evolution in Asian endemic Procapra gazelles.

    PubMed

    Hu, Junhua; Jiang, Zhigang; Chen, Jing; Qiao, Huijie

    2015-01-01

    Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system-based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species' bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification. PMID:25951051

  11. Morphological change in machines accelerates the evolution of robust behavior

    PubMed Central

    Bongard, Josh

    2011-01-01

    Most animals exhibit significant neurological and morphological change throughout their lifetime. No robots to date, however, grow new morphological structure while behaving. This is due to technological limitations but also because it is unclear that morphological change provides a benefit to the acquisition of robust behavior in machines. Here I show that in evolving populations of simulated robots, if robots grow from anguilliform into legged robots during their lifetime in the early stages of evolution, and the anguilliform body plan is gradually lost during later stages of evolution, gaits are evolved for the final, legged form of the robot more rapidly—and the evolved gaits are more robust—compared to evolving populations of legged robots that do not transition through the anguilliform body plan. This suggests that morphological change, as well as the evolution of development, are two important processes that improve the automatic generation of robust behaviors for machines. It also provides an experimental platform for investigating the relationship between the evolution of development and robust behavior in biological organisms. PMID:21220304

  12. Morphological change in machines accelerates the evolution of robust behavior.

    PubMed

    Bongard, Josh

    2011-01-25

    Most animals exhibit significant neurological and morphological change throughout their lifetime. No robots to date, however, grow new morphological structure while behaving. This is due to technological limitations but also because it is unclear that morphological change provides a benefit to the acquisition of robust behavior in machines. Here I show that in evolving populations of simulated robots, if robots grow from anguilliform into legged robots during their lifetime in the early stages of evolution, and the anguilliform body plan is gradually lost during later stages of evolution, gaits are evolved for the final, legged form of the robot more rapidly--and the evolved gaits are more robust--compared to evolving populations of legged robots that do not transition through the anguilliform body plan. This suggests that morphological change, as well as the evolution of development, are two important processes that improve the automatic generation of robust behaviors for machines. It also provides an experimental platform for investigating the relationship between the evolution of development and robust behavior in biological organisms.

  13. Accelerated molecular evolution of insect orthologues of ERG28/C14orf1: a link with ecdysteroid metabolism?

    PubMed

    Veitia, R A; Hurst, L D

    2001-04-01

    We have analysed the evolution of ERG28/C14orf1, a gene coding for a protein involved in sterol biosynthesis. While primary sequence of the protein is well conserved in all organisms able to synthesize sterols de novo, strong divergence is noticed in insects, which are cholesterol auxotrophs. In spite of this virtual acceleration, our analysis suggests that the insect orthologues are evolving today at rates similar to those of the remaining members of the family. A plausible way to explain this acceleration and subsequent stabilization is that Erg28 plays a role in at least two different pathways. Discontinuation of the cholesterogenesis pathway in insects allowed the protein to evolve as much as the function in the other pathway was not compromised.

  14. Transcriptomic insights into human brain evolution: acceleration, neutrality, heterochrony.

    PubMed

    Somel, Mehmet; Rohlfs, Rori; Liu, Xiling

    2014-12-01

    Primate brain transcriptome comparisons within the last 12 years have yielded interesting but contradictory observations on how the transcriptome evolves, and its adaptive role in human cognitive evolution. Since the human-chimpanzee common ancestor, the human prefrontal cortex transcriptome seems to have evolved more than that of the chimpanzee. But at the same time, most expression differences among species, especially those observed in adults, appear as consequences of neutral evolution at cis-regulatory sites. Adaptive expression changes in the human brain may be rare events involving timing shifts, or heterochrony, in specific neurodevelopmental processes. Disentangling adaptive and neutral expression changes, and associating these with human-specific features of the brain require improved methods, comparisons across more species, and further work on comparative development.

  15. 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.

  16. Test Sequence for Superconducting XFEL Cavities in the Accelerator Module Test Facility (AMTF) at DESY

    NASA Astrophysics Data System (ADS)

    Schaffran, J.; Petersen, B.; Reschke, D.; Swierblewski, J.

    The European XFEL is a new research facility currently under construction at DESY in the Hamburg area in Germany. From 2016 onwards, it will generate extremely intense X-ray flashes that will be used by researchers from all over the world. The main part of the superconducting European XFEL linear accelerator consists of 100 accelerator modules with 800 RF-cavities inside. The accelerator modules, superconducting magnets and cavities will be tested in the accelerator module test facility (AMTF) at DESY. This paper gives an overview of the test sequences for the superconducting cavities, applied in the preparation area and at the two cryostats (XATC) of the AMTF-hall, and describes the complete area. In addition it summarizes the tests and lessons learnt until the middle of 2014.

  17. Tropics accelerate the evolution of hybrid male sterility in Drosophila.

    PubMed

    Yukilevich, Roman

    2013-06-01

    Understanding the evolutionary mechanisms that facilitate speciation and explain global patterns of species diversity has remained a challenge for decades. The most general pattern of species biodiversity is the latitudinal gradient, whereby species richness increases toward the tropics. Although such a global pattern probably has a multitude of causes, recent attention has focused on the hypothesis that speciation and the evolution of reproductive isolation occur faster in the tropics. Here, I tested this prediction using a dataset on premating and postzygotic isolation between recently diverged Drosophila species. Results showed that while the evolution of premating isolation was not greater between tropical Drosophila relative to nontropical species, postzygotic isolation evolved faster in the tropics. In particular, hybrid male sterility was much greater among tropical Drosophila compared to nontropical species pairs of similar genetic age. Several testable explanations for the novel pattern are discussed, including greater role for sterility-inducing bacterial endosymbionts in the tropics and more intense sperm-sperm competition or sperm-egg sexual conflict in the tropics. The results imply that processes of speciation in the tropics may evolve at different rates or may even be somewhat different from those at higher latitudes.

  18. Clinical sequencing uncovers origins and evolution of Lassa virus

    PubMed Central

    Andersen, Kristian G.; Shapiro, B. Jesse; Matranga, Christian B.; Sealfon, Rachel; Lin, Aaron E.; Moses, Lina M.; Folarin, Onikepe A.; Goba, Augustine; Odia, Ikponmwonsa; Ehiane, Philomena E.; Momoh, Mambu; England, Eleina M.; Winnicki, Sarah; Branco, Luis M.; Gire, Stephen K.; Phelan, Eric; Tariyal, Ridhi; Tewhey, Ryan; Omoniwa, Omowunmi; Fullah, Mohammed; Fonnie, Richard; Fonnie, Mbalu; Kanneh, Lansana; Jalloh, Simbirie; Gbakie, Michael; Saffa, Sidiki; Karbo, Kandeh; Gladden, Adrianne D.; Qu, James; Stremlau, Matthew; Nekoui, Mahan; Finucane, Hilary K.; Tabrizi, Shervin; Vitti, Joseph J.; Birren, Bruce; Fitzgerald, Michael; McCowan, Caryn; Ireland, Andrea; Berlin, Aaron M.; Bochicchio, James; Tazon-Vega, Barbara; Lennon, Niall J.; Ryan, Elizabeth M.; Bjornson, Zach; Milner, Danny A.; Lukens, Amanda K.; Broodie, Nisha; Rowland, Megan; Heinrich, Megan; Akdag, Marjan; Schieffelin, John S.; Levy, Danielle; Akpan, Henry; Bausch, Daniel G.; Rubins, Kathleen; McCormick, Joseph B.; Lander, Eric S.; Günther, Stephan; Hensley, Lisa; Okogbenin, Sylvanus; Schaffner, Stephen F.; Okokhere, Peter O.; Khan, S. Humarr; Grant, Donald S.; Akpede, George O.; Asogun, Danny A.; Gnirke, Andreas; Levin, Joshua Z.; Happi, Christian T.; Garry, Robert F.; Sabeti, Pardis C.

    2015-01-01

    Summary The 2013-2015 West African epidemic of Ebola virus disease (EVD) reminds us how little is known about biosafety level-4 viruses. Like Ebola virus, Lassa virus (LASV) can cause hemorrhagic fever with high case fatality rates. We generated a genomic catalog of almost 200 LASV sequences from clinical and rodent reservoir samples. We show that whereas the 2013-2015 EVD epidemic is fueled by human-to-human transmissions, LASV infections mainly result from reservoir-to-human infections. We elucidated the spread of LASV across West Africa and show that this migration was accompanied by changes in LASV genome abundance, fatality rates, codon adaptation, and translational efficiency. By investigating intrahost evolution, we found that mutations accumulate in epitopes of viral surface proteins, suggesting selection for immune escape. This catalog will serve as a foundation for the development of vaccines and diagnostics. PMID:26276630

  19. Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

    PubMed

    Andersen, Kristian G; Shapiro, B Jesse; Matranga, Christian B; Sealfon, Rachel; Lin, Aaron E; Moses, Lina M; Folarin, Onikepe A; Goba, Augustine; Odia, Ikponmwonsa; Ehiane, Philomena E; Momoh, Mambu; England, Eleina M; Winnicki, Sarah; Branco, Luis M; Gire, Stephen K; Phelan, Eric; Tariyal, Ridhi; Tewhey, Ryan; Omoniwa, Omowunmi; Fullah, Mohammed; Fonnie, Richard; Fonnie, Mbalu; Kanneh, Lansana; Jalloh, Simbirie; Gbakie, Michael; Saffa, Sidiki; Karbo, Kandeh; Gladden, Adrianne D; Qu, James; Stremlau, Matthew; Nekoui, Mahan; Finucane, Hilary K; Tabrizi, Shervin; Vitti, Joseph J; Birren, Bruce; Fitzgerald, Michael; McCowan, Caryn; Ireland, Andrea; Berlin, Aaron M; Bochicchio, James; Tazon-Vega, Barbara; Lennon, Niall J; Ryan, Elizabeth M; Bjornson, Zach; Milner, Danny A; Lukens, Amanda K; Broodie, Nisha; Rowland, Megan; Heinrich, Megan; Akdag, Marjan; Schieffelin, John S; Levy, Danielle; Akpan, Henry; Bausch, Daniel G; Rubins, Kathleen; McCormick, Joseph B; Lander, Eric S; Günther, Stephan; Hensley, Lisa; Okogbenin, Sylvanus; Schaffner, Stephen F; Okokhere, Peter O; Khan, S Humarr; Grant, Donald S; Akpede, George O; Asogun, Danny A; Gnirke, Andreas; Levin, Joshua Z; Happi, Christian T; Garry, Robert F; Sabeti, Pardis C

    2015-08-13

    The 2013-2015 West African epidemic of Ebola virus disease (EVD) reminds us of how little is known about biosafety level 4 viruses. Like Ebola virus, Lassa virus (LASV) can cause hemorrhagic fever with high case fatality rates. We generated a genomic catalog of almost 200 LASV sequences from clinical and rodent reservoir samples. We show that whereas the 2013-2015 EVD epidemic is fueled by human-to-human transmissions, LASV infections mainly result from reservoir-to-human infections. We elucidated the spread of LASV across West Africa and show that this migration was accompanied by changes in LASV genome abundance, fatality rates, codon adaptation, and translational efficiency. By investigating intrahost evolution, we found that mutations accumulate in epitopes of viral surface proteins, suggesting selection for immune escape. This catalog will serve as a foundation for the development of vaccines and diagnostics. VIDEO ABSTRACT. PMID:26276630

  20. Primordial stellar evolution - The pre-main-sequence phase

    NASA Technical Reports Server (NTRS)

    Stahler, S. W.; Palla, F.; Salpeter, E. E.

    1986-01-01

    The quasi-static contraction of primordial stars composed of pure hydrogen and helium gas is studied by following numerically the evolution of a star of five solar masses from the end of protostellar accretion to the onset of hydrogen burning. Although the protostellar core of this mass is radiatively stable and undergoing nonhomologous contraction, its large surface area and luminosity force the star to a partially convective, homologously contracting state within only 100 yr. Deuterium later ignites at an off-center temperature maximum but fails to produce interior convection. The star follows a conventional premain sequence track in the HR diagram, reaching the ZAMS after 1.2 million yr, with a luminosity of 880 solar luminosities and a radius of 1.2 solar radii.

  1. Genome sequence of mungbean and insights into evolution within Vigna species.

    PubMed

    Kang, Yang Jae; Kim, Sue K; Kim, Moon Young; Lestari, Puji; Kim, Kil Hyun; Ha, Bo-Keun; Jun, Tae Hwan; Hwang, Won Joo; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Yoon, Min Young; Jang, Young Eun; Han, Kwang Soo; Taeprayoon, Puntaree; Yoon, Na; Somta, Prakit; Tanya, Patcharin; Kim, Kwang Soo; Gwag, Jae-Gyun; Moon, Jung-Kyung; Lee, Yeong-Ho; Park, Beom-Seok; Bombarely, Aureliano; Doyle, Jeffrey J; Jackson, Scott A; Schafleitner, Roland; Srinives, Peerasak; Varshney, Rajeev K; Lee, Suk-Ha

    2014-11-11

    Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

  2. Genome sequence of mungbean and insights into evolution within Vigna species

    PubMed Central

    Kang, Yang Jae; Kim, Sue K.; Kim, Moon Young; Lestari, Puji; Kim, Kil Hyun; Ha, Bo-Keun; Jun, Tae Hwan; Hwang, Won Joo; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Yoon, Min Young; Jang, Young Eun; Han, Kwang Soo; Taeprayoon, Puntaree; Yoon, Na; Somta, Prakit; Tanya, Patcharin; Kim, Kwang Soo; Gwag, Jae-Gyun; Moon, Jung-Kyung; Lee, Yeong-Ho; Park, Beom-Seok; Bombarely, Aureliano; Doyle, Jeffrey J.; Jackson, Scott A.; Schafleitner, Roland; Srinives, Peerasak; Varshney, Rajeev K.; Lee, Suk-Ha

    2014-01-01

    Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis. PMID:25384727

  3. Pre- and main-sequence evolution of solar activity

    NASA Technical Reports Server (NTRS)

    Walter, Frederick M.; Barry, Don C.

    1991-01-01

    The magnetic activity on single solarlike stars declines with stellar age. This has important consequences for the influence of the sun on the early solar system. What is meant by stellar activity, and how it is measured, is reviewed. Stellar activity on the premain-sequence phase of evolution is discussed; the classical T Tauri stars do not exhibit solarlike activity, while the naked T Tauri stars do. The emission surface fluxes of the naked T Tauri stars are similar to those of the youngest main-sequence G stars. The best representation for solarlike stars is a decay proportional to exp(A x t exp 0.5), where A is a function of line excitation temperature. From these decay laws, one can determine the interdependences of the activity, age, and rotation periods. The fluxes of ionizing photons at the earth early in its history are discussed; there was sufficient fluence to account for the observed isotopic ratios of the noble gases.

  4. PROFESS: a PROtein function, evolution, structure and sequence database.

    PubMed

    Triplet, Thomas; Shortridge, Matthew D; Griep, Mark A; Stark, Jaime L; Powers, Robert; Revesz, Peter

    2010-07-06

    The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are approximately 1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein-protein interaction networks. Database URL: http://cse.unl.edu/~profess/

  5. Constraints on pre-main-sequence evolution from stellar pulsations

    NASA Astrophysics Data System (ADS)

    Casey, M. P.; Zwintz, K.; Guenther, D. B.

    2014-02-01

    Pulsating pre-main-sequence (PMS) stars afford the earliest opportunity in the lifetime of a star to which the concepts of asteroseismology can be applied. PMS stars should be structurally simpler than their evolved counterparts, thus (hopefully!) making any asteroseismic analysis relatively easier. Unfortunately, this isn't necessarily the case. The majority of these stars (around 80) are δ Scuti pulsators, with a couple of γ Doradus, γ Doradus - δ Scuti hybrids, and slowly pulsating B stars thrown into the mix. The majority of these stars have only been discovered within the last ten years, with the community still uncovering the richness of phenomena associated with these stars, many of which defy traditional asteroseismic analysis. A systematic asteroseismic analysis of all of the δ Scuti PMS stars was performed in order to get a better handle on the properties of these stars as a group. Some strange results have been found, including one star pulsating up to the theoretical acoustic cut-off frequency of the star, and a number of stars in which the most basic asteroseismic analysis suggests problems with the stars' positions in the Hertzsprung-Russell diagram. From this we get an idea of the\\break constraints - or lack thereof - that these results can put on PMS stellar evolution.

  6. Latitudinal gradients in climatic-niche evolution accelerate trait evolution at high latitudes.

    PubMed

    Lawson, Adam M; Weir, Jason T

    2014-11-01

    Despite the importance of divergent selection to the speed of evolution, it remains poorly understood if divergent selection is more prevalent in the tropics (where species richness is highest), or at high latitudes (where paleoclimate change has been most intense). We tested whether the rate of climatic-niche evolution - one proxy for divergent selection - varies with latitude for 111 pairs of bird species. Using Brownian motion and Ornsetin-Ulhenbeck models, we show that evolutionary rates along two important axes of the climatic-niche - temperature and seasonality - have been faster at higher latitudes. We then tested whether divergence of the climatic-niche was associated with evolution in traits important in ecological differentiation (body mass) and reproductive isolation (song), and found that climatic divergence is associated with faster rates in both measures. These results highlight the importance of climate-mediated divergent selection pressures in driving evolutionary divergence and reproductive isolation at high latitudes. PMID:25168260

  7. Latitudinal gradients in climatic-niche evolution accelerate trait evolution at high latitudes.

    PubMed

    Lawson, Adam M; Weir, Jason T

    2014-11-01

    Despite the importance of divergent selection to the speed of evolution, it remains poorly understood if divergent selection is more prevalent in the tropics (where species richness is highest), or at high latitudes (where paleoclimate change has been most intense). We tested whether the rate of climatic-niche evolution - one proxy for divergent selection - varies with latitude for 111 pairs of bird species. Using Brownian motion and Ornsetin-Ulhenbeck models, we show that evolutionary rates along two important axes of the climatic-niche - temperature and seasonality - have been faster at higher latitudes. We then tested whether divergence of the climatic-niche was associated with evolution in traits important in ecological differentiation (body mass) and reproductive isolation (song), and found that climatic divergence is associated with faster rates in both measures. These results highlight the importance of climate-mediated divergent selection pressures in driving evolutionary divergence and reproductive isolation at high latitudes.

  8. Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function

    PubMed Central

    Mehrotra, Shweta; Goyal, Vinod

    2014-01-01

    Repetitive DNA sequences are a major component of eukaryotic genomes and may account for up to 90% of the genome size. They can be divided into minisatellite, microsatellite and satellite sequences. Satellite DNA sequences are considered to be a fast-evolving component of eukaryotic genomes, comprising tandemly-arrayed, highly-repetitive and highly-conserved monomer sequences. The monomer unit of satellite DNA is 150–400 base pairs (bp) in length. Repetitive sequences may be species- or genus-specific, and may be centromeric or subtelomeric in nature. They exhibit cohesive and concerted evolution caused by molecular drive, leading to high sequence homogeneity. Repetitive sequences accumulate variations in sequence and copy number during evolution, hence they are important tools for taxonomic and phylogenetic studies, and are known as “tuning knobs” in the evolution. Therefore, knowledge of repetitive sequences assists our understanding of the organization, evolution and behavior of eukaryotic genomes. Repetitive sequences have cytoplasmic, cellular and developmental effects and play a role in chromosomal recombination. In the post-genomics era, with the introduction of next-generation sequencing technology, it is possible to evaluate complex genomes for analyzing repetitive sequences and deciphering the yet unknown functional potential of repetitive sequences. PMID:25132181

  9. The Intervening Sequence of Coxiella burnetii: Characterization and Evolution

    PubMed Central

    Warrier, Indu; Walter, Mathias C.; Frangoulidis, Dimitrios; Raghavan, Rahul; Hicks, Linda D.; Minnick, Michael F.

    2016-01-01

    The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon is prone to change, and the S23p-encoding ORF is evidently undergoing reductive evolution. We determined that IVS excision from 23S rRNA was mediated by RNase III, and IVS RNA was rapidly degraded, thereafter. Levels of the resulting 23S rRNA fragments that flank the IVS, F1 (~1.2 kb) and F2 (~1.7 kb), were quantified over C. burnetii's logarithmic growth phase (1–5 d). Results showed that 23S F1 quantities were consistently higher than those of F2 and 16S rRNA. The disparity between levels of the two 23S rRNA fragments following excision of IVS is an interesting phenomenon of unknown significance. Based upon phylogenetic analyses, IVS was acquired through horizontal transfer after C. burnetii's divergence from an ancestral bacterium and has been subsequently maintained by vertical transfer. The widespread occurrence, maintenance and conservation of the IVS in C. burnetii imply that it plays an adaptive role or has a neutral effect on fitness.

  10. The Intervening Sequence of Coxiella burnetii: Characterization and Evolution.

    PubMed

    Warrier, Indu; Walter, Mathias C; Frangoulidis, Dimitrios; Raghavan, Rahul; Hicks, Linda D; Minnick, Michael F

    2016-01-01

    The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon is prone to change, and the S23p-encoding ORF is evidently undergoing reductive evolution. We determined that IVS excision from 23S rRNA was mediated by RNase III, and IVS RNA was rapidly degraded, thereafter. Levels of the resulting 23S rRNA fragments that flank the IVS, F1 (~1.2 kb) and F2 (~1.7 kb), were quantified over C. burnetii's logarithmic growth phase (1-5 d). Results showed that 23S F1 quantities were consistently higher than those of F2 and 16S rRNA. The disparity between levels of the two 23S rRNA fragments following excision of IVS is an interesting phenomenon of unknown significance. Based upon phylogenetic analyses, IVS was acquired through horizontal transfer after C. burnetii's divergence from an ancestral bacterium and has been subsequently maintained by vertical transfer. The widespread occurrence, maintenance and conservation of the IVS in C. burnetii imply that it plays an adaptive role or has a neutral effect on fitness. PMID:27595093

  11. The Intervening Sequence of Coxiella burnetii: Characterization and Evolution

    PubMed Central

    Warrier, Indu; Walter, Mathias C.; Frangoulidis, Dimitrios; Raghavan, Rahul; Hicks, Linda D.; Minnick, Michael F.

    2016-01-01

    The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon is prone to change, and the S23p-encoding ORF is evidently undergoing reductive evolution. We determined that IVS excision from 23S rRNA was mediated by RNase III, and IVS RNA was rapidly degraded, thereafter. Levels of the resulting 23S rRNA fragments that flank the IVS, F1 (~1.2 kb) and F2 (~1.7 kb), were quantified over C. burnetii's logarithmic growth phase (1–5 d). Results showed that 23S F1 quantities were consistently higher than those of F2 and 16S rRNA. The disparity between levels of the two 23S rRNA fragments following excision of IVS is an interesting phenomenon of unknown significance. Based upon phylogenetic analyses, IVS was acquired through horizontal transfer after C. burnetii's divergence from an ancestral bacterium and has been subsequently maintained by vertical transfer. The widespread occurrence, maintenance and conservation of the IVS in C. burnetii imply that it plays an adaptive role or has a neutral effect on fitness. PMID:27595093

  12. Evolution of Supermassive Black Hole Binaries and Acceleration of Jet Precession in Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Liu, F. K.; Chen, X.

    2007-12-01

    Supermassive black hole binaries (SMBHBs) are expected with the hierarchical galaxy formation model. Currently, physics processes dominating the evolution of a SMBHB are unclear. An interesting question is whether we could observationally determine the evolution of SMBHBs and give constraints on the physical processes. Jet precession has been observed in many active galactic nuclei (AGNs) and is generally attributed to disk precession. In this paper we calculate the time variation of jet precession and conclude that jet precession is accelerated in SMBHB systems but decelerated in others. The acceleration of jet precession, dPpr/dt, is related to the jet precession timescale, Ppr, and the SMBHB evolution timescale, τa, as dPpr/dt~=-Λ(Ppr/τa). Our calculations based on the models for jet precession and SMBHB evolution show that dPpr/dt can be as high as about -1.0, with a typical value of -0.2, and can be easily detected. We discuss the differential jet precession for NGC 1275 that has been observed in the literature. If its observed rapid acceleration of jet precession is true, the jet precession is due to the orbital motion of an unbound SMBHB with a mass ratio of q~0.76. When jets precess from ancient bubbles to the currently active jets, the separation of the SMBHB decreases from about 1.46 kpc to 0.80 kpc, with an averaged decreasing velocity of da/dt~=-1.54×106 cm s-1 and an evolution timescale of τa~7.5×107 yr. However, if we assume steady jet precession for many cycles, the observations imply a hard SMBHB with a mass ratio of a q~0.21 and a separation of a~0.29 pc.

  13. Fast T(2) relaxometry with an accelerated multi-echo spin-echo sequence.

    PubMed

    Sénégas, Julien; Liu, Wei; Dahnke, Hannes; Song, Hotaek; Jordan, E Kay; Frank, Joseph A

    2010-10-01

    A new method has been developed to reduce the number of phase-encoding steps in a multi-echo spin-echo imaging sequence allowing fast T(2) mapping without loss of spatial resolution. In the proposed approach, the k-space data at each echo time were undersampled and a reconstruction algorithm that exploited the temporal correlation of the MR signal in k-space was used to reconstruct alias-free images. A specific application of this algorithm with multiple-receiver acquisition, offering an alternative to existing parallel imaging methods, has also been introduced. The fast T(2) mapping method has been validated in human brain T(2) measurements in a group of nine volunteers with acceleration factors up to 3.4. The results demonstrated that the proposed method exhibited excellent linear correlation with the regular T(2) mapping with full sampling and achieved better image reconstruction and T(2) mapping with respect to SNR and reconstruction artifacts than the selected reference acceleration techniques. The new method has also been applied for quantitative tracking of injected magnetically labeled breast cancer cells in the rat brain with acceleration factors of 1.8 and 3.0. The proposed technique can provide an effective approach for accelerated T(2) quantification, especially for experiments with single-channel coil when parallel imaging is not applicable. PMID:20878973

  14. Universal Sequence Replication, Reversible Polymerization and Early Functional Biopolymers: A Model for the Initiation of Prebiotic Sequence Evolution

    PubMed Central

    Walker, Sara Imari; Grover, Martha A.; Hud, Nicholas V.

    2012-01-01

    Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles) that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for regularly varying monomer

  15. Does vocal learning accelerate acoustic diversification? Evolution of contact calls in Neotropical parrots.

    PubMed

    Medina-García, A; Araya-Salas, M; Wright, T F

    2015-10-01

    Learning has been traditionally thought to accelerate the evolutionary change of behavioural traits. We evaluated the evolutionary rate of learned vocalizations and the interplay of morphology and ecology in the evolution of these signals. We examined contact calls of 51 species of Neotropical parrots from the tribe Arini. Parrots are ideal subjects due to their wide range of body sizes and habitats, and their open-ended vocal learning that allows them to modify their calls throughout life. We estimated the evolutionary rate of acoustic parameters of parrot contact calls and compared them to those of morphological traits and habitat. We also evaluated the effect of body mass, bill length, vegetation density and species interactions on acoustic parameters of contact calls while controlling for phylogeny. Evolutionary rates of acoustic parameters did not differ from those of our predictor variables except for spectral entropy, which had a significantly slower rate of evolution. We found support for correlated evolution of call duration, and fundamental and peak frequencies with body mass, and of fundamental frequency with bill length. The degree of sympatry between species did not have a significant effect on acoustic parameters. Our results suggest that parrot contact calls, which are learned acoustic signals, show evolutionary rates similar to those of morphological traits. This is the first study to our knowledge to provide evidence that change through cultural evolution does not necessarily accelerate the evolutionary rate of traits acquired through life-long vocal learning.

  16. Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

    PubMed Central

    Poon, Art F. Y.; Swenson, Luke C.; Bunnik, Evelien M.; Edo-Matas, Diana; Schuitemaker, Hanneke; van 't Wout, Angélique B.; Harrigan, P. Richard

    2012-01-01

    At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a ‘fitness valley’ separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points) from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS). We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30) months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25) months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant. PMID:23133358

  17. Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data.

    PubMed

    Poon, Art F Y; Swenson, Luke C; Bunnik, Evelien M; Edo-Matas, Diana; Schuitemaker, Hanneke; van 't Wout, Angélique B; Harrigan, P Richard

    2012-01-01

    At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a 'fitness valley' separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points) from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS). We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30) months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25) months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant.

  18. Evolution of the Sequence Ontology terms and relationships

    PubMed Central

    Mungall, Christopher J.; Batchelor, Colin; Eilbeck, Karen

    2010-01-01

    The Sequence Ontology is an established ontology, with a large user community, for the purpose of genomic annotation. We are reforming the ontology to provide better terms and relationships to describe the features of biological sequence, for both genomic and derived sequence. The SO is working within the guidelines of the OBO Foundry to provide interoperability between SO and the other related OBO ontologies. Here we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence. PMID:20226267

  19. Accelerated Integrated Science Sequence: An Interdisciplinary Introductory Course for Science Majors

    PubMed Central

    Copp, Newton H.; Black, Kersey; Gould, Scot

    2012-01-01

    We report here on our development of an introductory science course sequence that integrates biology, chemistry and physics in order to foster an interdisciplinary perspective in future science majors. Accelerated Integrated Science Sequence (AISS) is a two semester, double credit sequence co-taught by a biologist, a physicist and a chemist to first year undergraduates who plan to major in a natural science field. Topics are organized within a thematic framework. The course sequence also features integration of various pedagogical approaches as students shift from one type of activity to another within the same class session. The presence of AISS in our curriculum over the past five years has been correlated with increased recruitment and graduation of students in science majors and a perception within the department that AISS has helped improve the culture of learning. These benefits outweigh the difficulties of developing such a course and encourage us that interdisciplinary introductory courses can make important contributions to training versatile scientists. PMID:23494601

  20. Evolution of prokaryote and eukaryote lines inferred from sequence evidence

    NASA Technical Reports Server (NTRS)

    Hunt, L. T.; George, D. G.; Yeh, L.-S.; Dayhoff, M. O.

    1984-01-01

    This paper describes the evolution of prokaryotes and early eukaryotes, including their symbiotic relationships, as inferred from phylogenetic trees of bacterial ferredoxin, 5S ribosomal RNA, ribulose-1,5-biphosphate carboxylase large chain, and mitochondrial cytochrome oxidase polypeptide II.

  1. Molecular Evolution of Multi-subunit RNA Polymerases: Sequence Analysis

    PubMed Central

    Lane, William J.; Darst, Seth A.

    2009-01-01

    Transcription in all cellular organisms is performed by multi-subunit, DNA-dependent RNA polymerases that synthesize RNA from DNA templates. Previous sequence and structural studies have elucidated the importance of shared regions common to all multi-subunit RNA polymerases. In addition RNA polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. We have created comprehensive multiple sequence alignments using all available sequence data for the multi-subunit RNA polymerase large subunits, including the bacterial β and β′ subunits and their homologues from archaebacterial RNA polymerases, the eukaryotic RNA polymerases I, II, and III, the nuclear-cytoplasmic large double-stranded DNA Virus RNA polymerases, and plant plastid RNA polymerases. In order to overcome technical difficulties inherent to the large subunit sequences, including large sequence length, small and large lineage-specific insertions, split subunits, and fused proteins, we created an automated and customizable sequence retrieval and processing system. In addition, we used our alignments to create a more expansive set of shared sequence regions and bacterial lineage-specific domain insertions. We also analyzed the intergenic gap between the bacterial β and β′ genes. PMID:19895820

  2. Analysis of genetic systems using experimental evolution and whole-genome sequencing

    PubMed Central

    Hegreness, Matthew; Kishony, Roy

    2007-01-01

    The application of whole-genome sequencing to the study of microbial evolution promises to reveal the complex functional networks of mutations that underlie adaptation. A recent study of parallel evolution in populations of Escherichia coli shows how adaptation involves both functional changes to specific proteins as well as global changes in regulation. PMID:17274841

  3. Evolution of morphology in UHMWPE following accelerated aging: the effect of heating rates.

    PubMed

    Kurtz, S M; Pruitt, L A; Crane, D J; Edidin, A A

    1999-07-01

    Accelerated aging methods are used to evaluate the oxidative stability of UHMWPE components for total joint replacements. In this study, we traced the evolution of the crystalline morphology during accelerated thermal aging of UHMWPE in air with the intent of explaining previous, counterintuitive heating rate effects. GUR4150HP extruded rod stock material was machined into miniature (0.5 mm thick) specimens that were either gamma irradiated in air or in nitrogen (27 +/- 3 kGy) or left unirradiated (control). Accelerated aging in an air furnace (at 80 degrees C, atmospheric pressure) was performed on half of the test samples at a heating rate of 0.1 degrees C/min and at 5 degrees C/min for the remaining half. Although the initial heating rate, as measured by changes in density, did influence the absolute degradation rate by up to 214%, the heating rate effect did not appear to influence the relative ranking of UHMWPE in terms of its oxidative stability. The heating rate effect is more consistent with a kinetic mechanism of the oxidation process than it is with a previously hypothesized diffusion mechanism. UHMWPE morphology, as characterized using a transmission electron microscope (TEM), demonstrated considerable rearrangement of the crystalline regions as a result of the accelerated aging. The stacking of the lamellae observed after accelerated aging was not consistent with the morphology of naturally aged UHMWPE components. The observed differences in crystalline morphology likely result from the enhanced mobility of the polymer chains due to thermal aging and may be analogous to an annealing process.

  4. Genome sequencing of the extinct Eurasian wild aurochs illuminates the phylogeography and evolution of cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Interrogation of modern and ancient bovine genome sequences provides a valuable model to study the evolution of cattle. Here, we analyse the first complete wild aurochs (Bos primigenius) genome sequence using DNA extracted from a ~ 6,750 year-old humerus bone retrieved from a cave site in Derbyshire...

  5. Genome survey sequencing provides clues into glucosinolate biosynthesis and flowering pathway evolution in allotetrapolyploid Brassica juncea

    PubMed Central

    2014-01-01

    Background Brassica juncea is an economically important vegetable crop in China, oil crop in India, condiment crop in Europe and selected for canola quality recently in Canada and Australia. B. juncea (2n = 36, AABB) is an allotetraploid derived from interspecific hybridization between B. rapa (2n = 20, AA) and B. nigra (2n = 16, BB), followed by spontaneous chromosome doubling. Results Comparative genome analysis by genome survey sequence (GSS) of allopolyploid B. juncea with B. rapa was carried out based on high-throughput sequencing approaches. Over 28.35 Gb of GSS data were used for comparative analysis of B. juncea and B. rapa, producing 45.93% reads mapping to the B. rapa genome with a high ratio of single-end reads. Mapping data suggested more structure variation (SV) in the B. juncea genome than in B. rapa. We detected 2,921,310 single nucleotide polymorphisms (SNPs) with high heterozygosity and 113,368 SVs, including 1-3 bp Indels, between B. juncea and B. rapa. Non-synonymous polymorphisms in glucosinolate biosynthesis genes may account for differences in glucosinolate biosynthesis and glucosinolate components between B. juncea and B. rapa. Furthermore, we identified distinctive vernalization-dependent and photoperiod-dependent flowering pathways coexisting in allopolyploid B. juncea, suggesting contribution of these pathways to adaptation for survival during polyploidization. Conclusions Taken together, we proposed that polyploidization has allowed for accelerated evolution of the glucosinolate biosynthesis and flowering pathways in B. juncea that likely permit the phenotypic variation observed in the crop. PMID:24502855

  6. Skeletal ossification and sequence heterochrony in xenarthran evolution.

    PubMed

    Hautier, Lionel; Weisbecker, Vera; Goswami, Anjali; Knight, Frank; Kardjilov, Nikolay; Asher, Robert J

    2011-01-01

    Previous analyses of how mammals vary in their ossification sequences have focused on monotremes, marsupials, and boreoeutherian placentals. Here, we focus on the sequence of cranial and postcranial ossification events during growth in the xenarthran skull and skeleton, including armadillos, anteaters, and sloths. We use two different methods to quantify sequence heterochrony: sequence analysis of variance (ANOVA) and event-paring/Parsimov. Our results indicate that Parsimov is conservative and does not detect clear heterochronic shifts between xenarthran and boreoeutherian placentals. Sequence-ANOVA performs better, but both methods exhibit sensitivity to the artifactual accumulation of ties. By controlling for ties and taking into account results that the methods have in common, our analysis suggests that xenarthrans significantly differ from other placentals by a late ossification of the sternum and an early ossification of the phalanges and pubis. We interpret these differences as showing that heterochrony plays a role in the skeletal development of xenarthrans, a change from previous studies that have emphasized the developmental homogeneity of the skeleton across placental mammals. PMID:23016907

  7. Evolution of tRNA-like sequences and genome variability.

    PubMed

    Frenkel, Felix E; Chaley, Maria B; Korotkov, Eugene V; Skryabin, Konstantin G

    2004-06-23

    Transfer RNA (tRNA)-like sequences were searched for in the nine basic taxonomic divisions of GenBank-121 (viruses, phages, bacteria, plants, invertebrates, vertebrates, rodents, mammals, and primates) by an original program package implementing a dynamic profile alignment approach for the genetic texts' analysis, in using 22 profiles of tRNAs of different isotypes. In total, 175,901 previously unknown tRNA-like sequences were revealed. The locations of the tRNA-likes were considered over the regions whose functional meaning is described by standard Feature Keys in GenBank. Many regions containing the tRNA-like sequences were recognized as known repeats. A mode of distribution of the tRNA-like sequences in a genome was proposed as expansion in a content of the various transposable elements. An analysis of the integrity of RNA polymerase III inner promoters in the tRNA-like sequences over the GenBank divisions has shown a high possibility of generating new copies of short interspersed nuclear element (SINE) repeats in all divisions, excepting primates. The numerous tRNA-likes found in the regions of RNA polymerase II promoters have suggested an adaptation of RNA polymerase III promoter to a binding of RNA polymerase II. PMID:15194190

  8. Skeletal ossification and sequence heterochrony in xenarthran evolution.

    PubMed

    Hautier, Lionel; Weisbecker, Vera; Goswami, Anjali; Knight, Frank; Kardjilov, Nikolay; Asher, Robert J

    2011-01-01

    Previous analyses of how mammals vary in their ossification sequences have focused on monotremes, marsupials, and boreoeutherian placentals. Here, we focus on the sequence of cranial and postcranial ossification events during growth in the xenarthran skull and skeleton, including armadillos, anteaters, and sloths. We use two different methods to quantify sequence heterochrony: sequence analysis of variance (ANOVA) and event-paring/Parsimov. Our results indicate that Parsimov is conservative and does not detect clear heterochronic shifts between xenarthran and boreoeutherian placentals. Sequence-ANOVA performs better, but both methods exhibit sensitivity to the artifactual accumulation of ties. By controlling for ties and taking into account results that the methods have in common, our analysis suggests that xenarthrans significantly differ from other placentals by a late ossification of the sternum and an early ossification of the phalanges and pubis. We interpret these differences as showing that heterochrony plays a role in the skeletal development of xenarthrans, a change from previous studies that have emphasized the developmental homogeneity of the skeleton across placental mammals.

  9. Accelerating Aerobic Sludge Granulation by Adding Dry Sewage Sludge Micropowder in Sequencing Batch Reactors.

    PubMed

    Li, Jun; Liu, Jun; Wang, Danjun; Chen, Tao; Ma, Ting; Wang, Zhihong; Zhuo, Weilong

    2015-08-01

    Micropowder (20-250 µm) made from ground dry waste sludge from a municipal sewage treatment plant was added in a sequencing batch reactor (R2), which was fed by synthetic wastewater with acetate as carbon source. Compared with the traditional SBR (R1), aerobic sludge granulation time was shortened 15 days in R2. Furthermore, filamentous bacteria in bulking sludge were controlled to accelerate aerobic granulation and form large granules. Correspondingly, the SVI decreased from 225 mL/g to 37 mL/g. X-ray Fluorescence (XRF) analysis demonstrated that Al and Si from the micropowder were accumulated in granules. A mechanism hypotheses for the acceleration of aerobic granulation by adding dry sludge micropowder is proposed: added micropowder acts as nuclei to induce bacterial attachment; dissolved matters from the micropowder increase abruptly the organic load for starved sludge to control overgrown filamentous bacteria as a framework for aggregation; increased friction from the movement of micropowder forces the filaments which extend outwards to shrink for shaping granules. PMID:26308025

  10. The tomato genome sequence provides insight into fleshy fruit evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genome of the inbred tomato cultivar ‘Heinz 1706’ was sequenced and assembled using a combination of Sanger and “next generation” technologies. The predicted genome size is ~900 Mb, consistent with prior estimates, of which 760 Mb were assembled in 91 scaffolds aligned to the 12 tomato chromosom...

  11. Rapid evolution of cis-regulatory sequences via local point mutations

    NASA Technical Reports Server (NTRS)

    Stone, J. R.; Wray, G. A.

    2001-01-01

    Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.

  12. Comprehensive analysis of animal TALE homeobox genes: new conserved motifs and cases of accelerated evolution.

    PubMed

    Mukherjee, Krishanu; Bürglin, Thomas R

    2007-08-01

    TALE homeodomain proteins are an ancient subgroup within the group of homeodomain transcription factors that play important roles in animal, plant, and fungal development. We have extracted the full complement of TALE superclass homeobox genes from the genome projects of seven protostomes, seven deuterostomes, and Nematostella. This was supplemented with TALE homeobox genes from additional species and phylogenetic analyses were carried out with 276 sequences. We found 20 homeobox genes and 4 pseudogenes in humans, 21 genes in mouse, 8 genes in Drosophila, and 5 genes plus one truncated gene in Caenorhabditis elegans. Apart from the previously identified TALE classes MEIS, PBC, IRO, and TGIF, a novel class is identified, termed MOHAWK (MKX). Further, we show that the MEIS class can be divided into two families, PREP and MEIS. Prep genes have previously only been described in vertebrates but are lacking in Drosophila. Here we identify orthologues in other insect taxa as well as in the cnidarian Nematostella. In C. elegans, a divergent Prep protein has lost the homeodomain. Full-length multiple sequence alignment of the protostome and deuterostome sequences allowed us to identify several novel conserved motifs within the MKX, TGIF, and MEIS classes. Phylogenetic analyses revealed fast-evolving PBC class genes; in particular, some X-linked PBC genes in nematodes are subject to rapid evolution. In addition, several instances of gene loss were identified. In conclusion, our comprehensive analysis provides a defining framework for the classification of animal TALE homeobox genes and the understanding of their evolution.

  13. GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering.

    PubMed

    Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

    2016-01-01

    Sequence homology searches are used in various fields and require large amounts of computation time, especially for metagenomic analysis, owing to the large number of queries and the database size. To accelerate computing analyses, graphics processing units (GPUs) are widely used as a low-cost, high-performance computing platform. Therefore, we mapped the time-consuming steps involved in GHOSTZ, which is a state-of-the-art homology search algorithm for protein sequences, onto a GPU and implemented it as GHOSTZ-GPU. In addition, we optimized memory access for GPU calculations and for communication between the CPU and GPU. As per results of the evaluation test involving metagenomic data, GHOSTZ-GPU with 12 CPU threads and 1 GPU was approximately 3.0- to 4.1-fold faster than GHOSTZ with 12 CPU threads. Moreover, GHOSTZ-GPU with 12 CPU threads and 3 GPUs was approximately 5.8- to 7.7-fold faster than GHOSTZ with 12 CPU threads. PMID:27482905

  14. GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering

    PubMed Central

    Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

    2016-01-01

    Sequence homology searches are used in various fields and require large amounts of computation time, especially for metagenomic analysis, owing to the large number of queries and the database size. To accelerate computing analyses, graphics processing units (GPUs) are widely used as a low-cost, high-performance computing platform. Therefore, we mapped the time-consuming steps involved in GHOSTZ, which is a state-of-the-art homology search algorithm for protein sequences, onto a GPU and implemented it as GHOSTZ-GPU. In addition, we optimized memory access for GPU calculations and for communication between the CPU and GPU. As per results of the evaluation test involving metagenomic data, GHOSTZ-GPU with 12 CPU threads and 1 GPU was approximately 3.0- to 4.1-fold faster than GHOSTZ with 12 CPU threads. Moreover, GHOSTZ-GPU with 12 CPU threads and 3 GPUs was approximately 5.8- to 7.7-fold faster than GHOSTZ with 12 CPU threads. PMID:27482905

  15. The evolution processes of DNA sequences, languages and carols

    NASA Astrophysics Data System (ADS)

    Hauck, Jürgen; Henkel, Dorothea; Mika, Klaus

    2001-04-01

    The sequences of bases A, T, C and G of about 100 enolase, secA and cytochrome DNA were analyzed for attractive or repulsive interactions by the numbers T 1,T 2,T 3; r of nearest, next-nearest and third neighbor bases of the same kind and the concentration r=other bases/analyzed base. The area of possible T1, T2 values is limited by the linear borders T 2=2T 1-2, T 2=0 or T1=0 for clustering, attractive or repulsive interactions and the border T2=-2 T1+2(2- r) for a variation from repulsive to attractive interactions at r⩽2. Clustering is preferred by most bases in sequences of enolases and secA’ s. Major deviations with repulsive interactions of some bases are observed for archaea bacteria in secA and for highly developed animals and the human species in enolase sequences. The borders of the structure map for enthalpy stabilized structures with maximum interactions are approached in few cases. Most letters of the natural languages and some music notes are at the borders of the structure map.

  16. Nonrandomness in protein sequences: evidence for a physically driven stage of evolution?

    PubMed Central

    Pande, V S; Grosberg, A Y; Tanaka, T

    1994-01-01

    The sequences, or primary structures, of existing biopolymers--in particular, proteins--are believed to be a product of evolution. Are the sequences random? If not, what is the character of this nonrandomness? To explore the statistics of protein sequences, we use the idea of mapping the sequence onto the trajectory of a random walk, originally proposed by Peng et al. [Peng, C.-K., Buldyrev, S. V., Goldberger, A. L., Havlin, S., Sciortino, F., Simons, M. & Stanley, H. E. (1992) Nature (London) 356, 168-170] in their analysis of DNA sequences. Using three different mappings, corresponding to three basic physical interactions between amino acids, we found pronounced deviations from pure randomness, and these deviations seem directed toward minimization of the energy of the three-dimensional structure. We consider this result as evidence for a physically driven stage of evolution. Images Fig. 1 Fig. 2 Fig. 3 PMID:7809157

  17. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

    PubMed Central

    Richards, Stephen; Liu, Yue; Bettencourt, Brian R.; Hradecky, Pavel; Letovsky, Stan; Nielsen, Rasmus; Thornton, Kevin; Hubisz, Melissa J.; Chen, Rui; Meisel, Richard P.; Couronne, Olivier; Hua, Sujun; Smith, Mark A.; Zhang, Peili; Liu, Jing; Bussemaker, Harmen J.; van Batenburg, Marinus F.; Howells, Sally L.; Scherer, Steven E.; Sodergren, Erica; Matthews, Beverly B.; Crosby, Madeline A.; Schroeder, Andrew J.; Ortiz-Barrientos, Daniel; Rives, Catharine M.; Metzker, Michael L.; Muzny, Donna M.; Scott, Graham; Steffen, David; Wheeler, David A.; Worley, Kim C.; Havlak, Paul; Durbin, K. James; Egan, Amy; Gill, Rachel; Hume, Jennifer; Morgan, Margaret B.; Miner, George; Hamilton, Cerissa; Huang, Yanmei; Waldron, Lenée; Verduzco, Daniel; Clerc-Blankenburg, Kerstin P.; Dubchak, Inna; Noor, Mohamed A.F.; Anderson, Wyatt; White, Kevin P.; Clark, Andrew G.; Schaeffer, Stephen W.; Gelbart, William; Weinstock, George M.; Gibbs, Richard A.

    2005-01-01

    We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25–55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species—but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila. PMID:15632085

  18. [Evolution of non-coding nucleotide sequences in Newcastle disease virus genomes ].

    PubMed

    Xu, Huaiying; Qin, Zhuoming; Qi, Lihong; Zhang, Wei; Wang, Youling; Liu, Jinhua

    2014-09-01

    [OBJECTIVE] Although much is done in the coding genes of Newcastle disease virus (NDV) , limited papers can be found with non-coding sequences. In this paper, the evolution tendency of non-coding sequences was studied. [METHODS] NDV strain LC12 isolated from duck with egg drop syndrome in 2012, and others 35 strains genome cDNA of different NDV genotype were sought and obtained from GenBank. Analytical approaches including nucleotide homology, nucleotide alignment and phylogenetic tree were associated with the leading sequences, trailer sequences, intergenic sequences (IGS), and coding gene between 5 'and 3' UTR nucleotide, respectively. [RESULTS] The location and the length of the non-coding sequences highly conserve, and the variation trend of non-coding sequences is synchronous with the entire genomes and coding genes. [ CONCLUSION] The molecular variation of the coding gene was indistinguishable with the non-coding gene in view of the NDV genome. PMID:25522596

  19. Evolution from primordial oligomeric repeats to modern coding sequences.

    PubMed

    Ohno, S

    1987-01-01

    It seems as though nature was most innovative at the very beginning of life on this Earth a few billion years ago. For example, the functional competence of most, if not all, of the sugar-metabolizing enzymes was clearly established before the division of eukaryotes from prokaryotes eons ago, each critical active-site amino acid sequence being conserved ever since by bacteria as well as by mammals. I contend that this initial innovativeness was due to the first set of coding sequences being repeats of base oligomers, thus encoding polypeptide chains of various periodicities; such periodical polypeptide chains can easily acquire alpha-helical and beta-sheet-forming segments. In fact, the entire length of sugar-metabolizing enzymes is comprised of alternating alpha-helical and beta-sheet-forming segments. In the prebiotic (therefore nonenzymatic) replication of nucleic acids, what was in short supply was long templates, for there apparently was no inherent obstacle in copying of long templates, if such existed, in the presence of Zn2+. I submit that in this prebiotic condition, only those nucleotide oligomers that were internal doubles were automatically assured of progressive elongation to become long templates. For example, a decamer that was a pentameric repeat and its complementary sequence may pair unequally to initiate the next round of replication: first unit pairing with second, and a paired segment serving as a primer. As a consequence of this unequal pairing, decameric templates managed to become pentadecameric templates only after one round of replication, and this elongation process had no inherent limit.

  20. Molecular co-catalyst accelerating hole transfer for enhanced photocatalytic H2 evolution

    PubMed Central

    Bi, Wentuan; Li, Xiaogang; Zhang, Lei; Jin, Tao; Zhang, Lidong; Zhang, Qun; Luo, Yi; Wu, Changzheng; Xie, Yi

    2015-01-01

    In artificial photocatalysis, sluggish kinetics of hole transfer and the resulting high-charge recombination rate have been the Achilles' heel of photocatalytic conversion efficiency. Here we demonstrate water-soluble molecules as co-catalysts to accelerate hole transfer for improved photocatalytic H2 evolution activity. Trifluoroacetic acid (TFA), by virtue of its reversible redox couple TFA·/TFA−, serves as a homogeneous co-catalyst that not only maximizes the contact areas between co-catalysts and reactants but also greatly promotes hole transfer. Thus K4Nb6O17 nanosheet catalysts achieve drastically increased photocatalytic H2 production rate in the presence of TFA, up to 32 times with respect to the blank experiment. The molecular co-catalyst represents a new, simple and highly effective approach to suppress recombination of photogenerated charges, and has provided fertile new ground for creating high-efficiency photosynthesis systems, avoiding use of noble-metal co-catalysts. PMID:26486863

  1. Molecular co-catalyst accelerating hole transfer for enhanced photocatalytic H2 evolution

    NASA Astrophysics Data System (ADS)

    Bi, Wentuan; Li, Xiaogang; Zhang, Lei; Jin, Tao; Zhang, Lidong; Zhang, Qun; Luo, Yi; Wu, Changzheng; Xie, Yi

    2015-10-01

    In artificial photocatalysis, sluggish kinetics of hole transfer and the resulting high-charge recombination rate have been the Achilles' heel of photocatalytic conversion efficiency. Here we demonstrate water-soluble molecules as co-catalysts to accelerate hole transfer for improved photocatalytic H2 evolution activity. Trifluoroacetic acid (TFA), by virtue of its reversible redox couple TFA./TFA-, serves as a homogeneous co-catalyst that not only maximizes the contact areas between co-catalysts and reactants but also greatly promotes hole transfer. Thus K4Nb6O17 nanosheet catalysts achieve drastically increased photocatalytic H2 production rate in the presence of TFA, up to 32 times with respect to the blank experiment. The molecular co-catalyst represents a new, simple and highly effective approach to suppress recombination of photogenerated charges, and has provided fertile new ground for creating high-efficiency photosynthesis systems, avoiding use of noble-metal co-catalysts.

  2. Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes of Acricotopus.

    PubMed

    Staiber, Wolfgang

    2004-08-01

    The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%-100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.

  3. The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape

    PubMed Central

    Yousaf, Aisha; Sohail Raza, Muhammad; Ali Abbasi, Amir

    2015-01-01

    Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates’ conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water–land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods’ enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land. PMID:26253316

  4. The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape.

    PubMed

    Yousaf, Aisha; Sohail Raza, Muhammad; Ali Abbasi, Amir

    2015-08-06

    Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates' conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water-land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods' enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land.

  5. SHOCK ACCELERATION OF PARTICLES IN THE NONSTATIONARY EVOLUTION OF COROTATING INTERACTION REGIONS

    SciTech Connect

    Tsubouchi, K.

    2011-10-20

    One-dimensional hybrid simulations are used to investigate the particle energization process during the nonstationary evolution of corotating interaction regions (CIRs) in the heliosphere. The simulation model, where fast and slow solar wind streams interact with each other, allows the formation of a pair (forward/reverse) of shocks at the CIR boundaries and the stream interface interior, which prevents the interchange of both streams. While both shocks are quasi-perpendicular and are not capable of accelerating thermal particles (hundreds of eV) up to a suprathermal energy (tens to hundreds of keV) in the early phase of their development, the reverse shock in the fast wind experiences a transition to a quasi-parallel regime in the later phase. The quasi-parallel reverse shock can efficiently accelerate particles to the suprathermal range. The different timescale of the adiabatic expansion between the fast and slow wind leads to a transition of the shock geometry that can take place more easily in the reverse shock than in the forward shock, where the magnetic field in the fast wind remains more radial to the propagation direction than in the slow wind. The difference in the acceleration efficiency between these shocks follows a well-known observed asymmetry in the profile of the energetic particle fluxes, where the larger intensity increases more in the reverse shock than in the forward shock. The present results suggest that the solar wind thermal plasma, as well as interstellar pickup ions, can contribute to the composition of energetic particles associated with the CIRs.

  6. A New Branch on the Tree: Next-Generation Sequencing in the Study of Cancer Evolution

    PubMed Central

    Brosnan, Jacqueline A.; Iacobuzio-Donahue, Christine A.

    2012-01-01

    Cancer is a disease caused by the accumulation of genetic alterations in association with successive waves of clonal expansion. Mapping of the human genome sequence, in conjunction with technical advances in the ability to sequence entire genomes, have provided new insight into the mutational spectra and genetic events associated with clonal evolution of cancer. Moving forward, a clearer understanding of those alterations that undergo positive and negative selection throughout carcinogenesis and leading to metastatic dissemination would provide a boon not only to our understanding of cancer evolution, but to the development of potential targets for therapeutic intervention as well. PMID:22245832

  7. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    SciTech Connect

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  8. Genome sequence of the brown Norway rat yields insights into mammalian evolution

    SciTech Connect

    Gibbs, Richard A.; Weinstock, George M.; Metzker, Michael L.; Muzny, Donna M.; Sodergren, Erica J.; Scherer, Steven; Scott, Graham; Steffen, David; Worley, Kim C.; Burch, Paula E.; Okwuonu, Geoffrey; Hines, Sandra; Lewis, Lora; DeRamo, Christine; Delgado, Oliver; Dugan-Rocha, Shannon; Miner, George; Morgan, Margaret; Hawes, Alicia; Gill, Rachel; Holt, Robert A.; Adams, Mark D.; Amanatides, Peter G.; Baden-Tillson, Holly; Barnstead, Mary; Chin, Soo; Evans, Cheryl A.; Ferriera, Steven; Fosler, Carl; Glodek, Anna; Gu, Zhiping; Jennings, Don; Kraft, Cheryl L.; Nguyen, Trixie; Pfannkoch, Cynthia M.; Sitter, Cynthia; Sutton, Granger G.; Venter, J. Craig; Woodage, Trevor; Smith, Douglas; Lee, Hong-Maei; Gustafson, Erik; Cahill, Patrick; Kana, Arnold; Doucette-Stamm, Lynn; Weinstock, Keith; Fechtel, Kim; Weiss, Robert B.; Dunn, Diane M.; Green, Eric D.; Blakesley, Robert W.; Bouffard, Gerard G.; de Jong, Pieter J.; Osoegawa, Kazutoyo; Zhu, Baoli; Marra, Marco; Schein, Jacqueline; Bosdet, Ian; Fjell, Chris; Jones, Steven; Krzywinski, Martin; Mathewson, Carrie; Siddiqui, Asim; Wye, Natasja; McPherson, John; Zhao, Shaying; Fraser, Claire M.; Shetty, Jyoti; Shatsman, Sofiya; Geer, Keita; Chen, Yixin; Abramzon, Sofyia; Nierman, William C.; Havlak, Paul H.; Chen, Rui; Durbin, K. James; Egan, Amy; Ren, Yanru; Song, Xing-Zhi; Li, Bingshan; Liu, Yue; Qin, Xiang; Cawley, Simon; Cooney, A.J.; D'Souza, Lisa M.; Martin, Kirt; Wu, Jia Qian; Gonzalez-Garay, Manuel L.; Jackson, Andrew R.; Kalafus, Kenneth J.; McLeod, Michael P.; Milosavljevic, Aleksandar; Virk, Davinder; Volkov, Andrei; Wheeler, David A.; Zhang, Zhengdong; Bailey, Jeffrey A.; Eichler, Evan E.; Tuzun, Eray; Birney, Ewan; Mongin, Emmanuel; Ureta-Vidal, Abel; Woodwark, Cara; Zdobnov, Evgeny; Bork, Peer; Suyama, Mikita; Torrents, David; Alexandersson, Marina; Trask, Barbara J.; Young, Janet M.; et al.

    2004-02-02

    The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90 percent of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

  9. INTERNAL STRUCTURE OF PROTOCLUSTER GALAXIES: ACCELERATED STRUCTURAL EVOLUTION IN OVERDENSE ENVIRONMENTS?

    SciTech Connect

    Zirm, Andrew W.; Toft, Sune; Tanaka, Masayuki E-mail: sune@dark-cosmology.dk

    2012-01-10

    We present a high spatial resolution Hubble Space Telescope/NICMOS imaging survey in the field of a known protocluster surrounding the powerful radio galaxy MRC1138-262 at z = 2.16. Previously, we have shown that this field exhibits a substantial surface overdensity of red J-H galaxies. Here we focus on the stellar masses and galaxy effective radii in an effort to compare and contrast the properties of likely protocluster galaxies with their field counterparts and to look for correlations between galaxy structure and (projected) distance relative to the radio galaxy. We find a hint that quiescent, cluster galaxies are on average less dense than quiescent field galaxies of similar stellar mass and redshift. In fact, we find that only two (of eight) quiescent protocluster galaxies are of similar density to the majority of the massive, quiescent compact galaxies (Semi-Evolved Elephantine Dense galaxies; SEEDs) found in several field surveys. Furthermore, there is some indication that the structural Sersic n parameter is higher (n {approx} 3-4) on average for cluster galaxies compared to the field SEEDs (n {approx} 1-2). This result may imply that the accelerated galaxy evolution expected (and observed) in overdense regions also extends to structural evolution presuming that massive galaxies began as dense (low n) SEEDs and have already evolved to be more in line with local galaxies of the same stellar mass.

  10. Evolution of branched regulatory genetic pathways: directional selection on pleiotropic loci accelerates developmental system drift.

    PubMed

    Johnson, Norman A; Porter, Adam H

    2007-01-01

    Developmental systems are regulated by a web of interacting loci. One common and useful approach in studying the evolution of development is to focus on classes of interacting elements within these systems. Here, we use individual-based simulations to study the evolution of traits controlled by branched developmental pathways involving three loci, where one locus regulates two different traits. We examined the system under a variety of selective regimes. In the case where one branch was under stabilizing selection and the other under directional selection, we observed "developmental system drift": the trait under stabilizing selection showed little phenotypic change even though the loci underlying that trait showed considerable evolutionary divergence. This occurs because the pleiotropic locus responds to directional selection and compensatory mutants are then favored in the pathway under stabilizing selection. Though developmental system drift may be caused by other mechanisms, it seems likely that it is accelerated by the same underlying genetic mechanism as that producing the Dobzhansky-Muller incompatibilities that lead to speciation in both linear and branched pathways. We also discuss predictions of our model for developmental system drift and how different selective regimes affect probabilities of speciation in the branched pathway system.

  11. Cubozoan crystallins: evidence for convergent evolution of pax regulatory sequences.

    PubMed

    Kozmik, Zbynek; Swamynathan, Shivalingappa K; Ruzickova, Jana; Jonasova, Kristyna; Paces, Vaclav; Vlcek, Cestmir; Piatigorsky, Joram

    2008-01-01

    Cnidaria is the earliest-branching metazoan phylum containing a well-developed, lens-containing visual system located on specialized sensory structures called rhopalia. Each rhopalium in a cubozoan jellyfish Tripedalia cystophora has a large and a small complex, camera-type eye with a cellular lens containing distinct families of crystallins. Here, we have characterized J2-crystallin and its gene in T. cystophora. The J2-crystallin gene is composed of a single exon and encodes a 157-amino acid cytoplasmic protein with no apparent homology to known proteins from other species. The non-lens expression of J2-crystallin suggests nonoptical as well as crystallin functions consistent with the gene-sharing strategy that has been used during evolution of lens crystallins in other invertebrates and vertebrates. Although nonfunctional in transfected mammalian lens cells, the J2-crystallin promoter is activated by the jellyfish paired domain transcription factor PaxB in co-transfection tests via binding to three paired domain sites. PaxB paired domain-binding sites were also identified in the PaxB-regulated promoters of the J1A- and J1B-crystallin genes, which are not homologous to the J2-crystallin gene. Taken together with previous studies on the regulation of the diverse crystallin genes, the present report strongly supports the idea that crystallin recruitment of multifunctional proteins was driven by convergent changes involving Pax (as well as other transcription factors) in the promoters of nonhomologous genes within and between species as well as within gene families. PMID:18184357

  12. The Norway spruce genome sequence and conifer genome evolution.

    PubMed

    Nystedt, Björn; Street, Nathaniel R; Wetterbom, Anna; Zuccolo, Andrea; Lin, Yao-Cheng; Scofield, Douglas G; Vezzi, Francesco; Delhomme, Nicolas; Giacomello, Stefania; Alexeyenko, Andrey; Vicedomini, Riccardo; Sahlin, Kristoffer; Sherwood, Ellen; Elfstrand, Malin; Gramzow, Lydia; Holmberg, Kristina; Hällman, Jimmie; Keech, Olivier; Klasson, Lisa; Koriabine, Maxim; Kucukoglu, Melis; Käller, Max; Luthman, Johannes; Lysholm, Fredrik; Niittylä, Totte; Olson, Ake; Rilakovic, Nemanja; Ritland, Carol; Rosselló, Josep A; Sena, Juliana; Svensson, Thomas; Talavera-López, Carlos; Theißen, Günter; Tuominen, Hannele; Vanneste, Kevin; Wu, Zhi-Qiang; Zhang, Bo; Zerbe, Philipp; Arvestad, Lars; Bhalerao, Rishikesh; Bohlmann, Joerg; Bousquet, Jean; Garcia Gil, Rosario; Hvidsten, Torgeir R; de Jong, Pieter; MacKay, John; Morgante, Michele; Ritland, Kermit; Sundberg, Björn; Thompson, Stacey Lee; Van de Peer, Yves; Andersson, Björn; Nilsson, Ove; Ingvarsson, Pär K; Lundeberg, Joakim; Jansson, Stefan

    2013-05-30

    Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

  13. Diagnosis of bubble evolution in laser-wakefield acceleration via angular distributions of betatron x-rays

    SciTech Connect

    Ma, Y.; Chen, L. M. Huang, K.; Yan, W. C.; Hafz, N. A. M.; Zhang, J.; Li, D. Z.; Dunn, J.; Sheng, Z. M.

    2014-10-20

    We present an indirect method to diagnose the electron beam behaviors and bubble dynamic evolution in a laser-wakefield accelerator. Four kinds of typical bubble dynamic evolution and, hence, electron beam behaviors observed in Particle-In-Cell simulations are identified correspondingly by simultaneous measurement of distinct angular distributions of the betatron radiation and electron beam energy spectra in experiment. The reconstruction of the bubble evolution may shed light on finding an effective way to better generate high-quality electron beams and enhanced betatron X-rays.

  14. The genome sequence of taurine cattle: A window to ruminant biology and evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (ma...

  15. Conservation of plastid sequences in the plant nuclear genome for millions of years facilitates endosymbiotic evolution.

    PubMed

    Rousseau-Gueutin, Mathieu; Ayliffe, Michael A; Timmis, Jeremy N

    2011-12-01

    The nuclear genome of eukaryotes contains large amounts of cytoplasmic organelle DNA (nuclear integrants of organelle DNA [norgs]). The recent sequencing of many mitochondrial and chloroplast genomes has enabled investigation of the potential role of norgs in endosymbiotic evolution. In this article, we describe a new polymerase chain reaction-based method that allows the identification and evolutionary study of recent and older norgs in a range of eukaryotes. We tested this method in the genus Nicotiana and obtained sequences from seven nuclear integrants of plastid DNA (nupts) totaling 25 kb in length. These nupts were estimated to have been transferred 0.033 to 5.81 million years ago. The spectrum of mutations present in the potential protein-coding sequences compared with the noncoding sequences of each nupt revealed that nupts evolve in a nuclear-specific manner and are under neutral evolution. Indels were more frequent in noncoding regions than in potential coding sequences of former chloroplastic DNA, most probably due to the presence of a higher number of homopolymeric sequences. Unexpectedly, some potential protein-coding sequences within the nupts still contained intact open reading frames for up to 5.81 million years. These results suggest that chloroplast genes transferred to the nucleus have in some cases several millions of years to acquire nuclear regulatory elements and become functional. The different factors influencing this time frame and the potential role of nupts in endosymbiotic gene transfer are discussed.

  16. Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution

    SciTech Connect

    Richards, Stephen; Liu, Yue; Bettencourt, Brian R.; Hradecky, Pavel; Letovsky, Stan; Nielsen, Rasmus; Thornton, Kevin; Todd, Melissa J.; Chen, Rui; Meisel, Richard P.; Couronne, Olivier; Hua, Sujun; Smith, Mark A.; Bussemaker, Harmen J.; van Batenburg, Marinus F.; Howells, Sally L.; Scherer, Steven E.; Sodergren, Erica; Matthews, Beverly B.; Crosby, Madeline A.; Schroeder, Andrew J.; Ortiz-Barrientos, Daniel; Rives, Catherine M.; Metzker, Michael L.; Muzny, Donna M.; Scott, Graham; Steffen, David; Wheeler, David A.; Worley, Kim C.; Havlak, Paul; Durbin, K. James; Egan, Amy; Gill, Rachel; Hume, Jennifer; Morgan, Margaret B.; Miner, George; Hamilton, Cerissa; Huang, Yanmei; Waldron, Lenee; Verduzco, Daniel; Blankenburg, Kerstin P.; Dubchak, Inna; Noor, Mohamed A.F.; Anderson, Wyatt; White, Kevin P.; Clark, Andrew G.; Schaeffer, Stephen W.; Gelbart, William; Weinstock, George M.; Gibbs, Richard A.

    2004-04-01

    The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

  17. Concerted evolution at the population level: pupfish HindIII satellite DNA sequences.

    PubMed Central

    Elder, J F; Turner, B J

    1994-01-01

    The canonical monomers (approximately 170 bp) of an abundant (1.9 x 10(6) copies per diploid genome) satellite DNA sequence family in the genome of Cyprinodon variegatus, a "pupfish" that ranges along the Atlantic coast from Cape Cod to central Mexico, are divergent in base sequence in 10 of 12 samples collected from natural populations. The divergence involves substitutions, deletions, and insertions, is marked in scope (mean pairwise sequence similarity = 61.6%; range = 35-95.9%), is largely confined to the 3' half of the monomer, and is not correlated with the distance among collecting sites. Repetitive cloning and direct genomic sequencing experiments failed to detect intrapopulation and intraindividual variation, suggesting high levels of sequence homogeneity within populations. The satellite sequence has therefore undergone "concerted evolution," at the level of the local population. Concerted evolution has previously almost always been discussed in terms of the divergence of species or higher taxa; its intraspecific occurrence apparently has not been reported previously. The generality of the observation is difficult to evaluate, for although satellite DNAs from a large number of organisms have been studied in detail, there appear to be little or no other data on their sequence variation in natural populations. The relationship (if any) between concerted, population level, satellite DNA divergence and the extent of gene flow/genetic isolation among conspecific natural populations remains to be established. Images PMID:8302879

  18. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.

    PubMed

    Groussin, M; Boussau, B; Gouy, M

    2013-07-01

    Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.

  19. Evolution of Endogenous Sequences of Banana Streak Virus: What Can We Learn from Banana (Musa sp.) Evolution?▿

    PubMed Central

    Gayral, Philippe; Blondin, Laurence; Guidolin, Olivier; Carreel, Françoise; Hippolyte, Isabelle; Perrier, Xavier; Iskra-Caruana, Marie-Line

    2010-01-01

    Endogenous plant pararetroviruses (EPRVs) are viral sequences of the family Caulimoviridae integrated into the nuclear genome of numerous plant species. The ability of some endogenous sequences of Banana streak viruses (eBSVs) in the genome of banana (Musa sp.) to induce infections just like the virus itself was recently demonstrated (P. Gayral et al., J. Virol. 83:6697-6710, 2008). Although eBSVs probably arose from accidental events, infectious eBSVs constitute an extreme case of parasitism, as well as a newly described strategy for vertical virus transmission in plants. We investigated the early evolutionary stages of infectious eBSV for two distinct BSV species—GF (BSGFV) and Imové (BSImV)—through the study of their distribution, insertion polymorphism, and structure evolution among selected banana genotypes representative of the diversity of 60 wild Musa species and genotypes. To do so, the historical frame of host evolution was analyzed by inferring banana phylogeny from two chloroplast regions—matK and trnL-trnF—as well as from the nuclear genome, using 19 microsatellite loci. We demonstrated that both BSV species integrated recently in banana evolution, circa 640,000 years ago. The two infectious eBSVs were subjected to different selective pressures and showed distinct levels of rearrangement within their final structure. In addition, the molecular phylogenies of integrated and nonintegrated BSVs enabled us to establish the phylogenetic origins of eBSGFV and eBSImV. PMID:20427523

  20. Human microRNAs originated from two periods at accelerated rates in mammalian evolution.

    PubMed

    Iwama, Hisakazu; Kato, Kiyohito; Imachi, Hitomi; Murao, Koji; Masaki, Tsutomu

    2013-03-01

    MicroRNAs (miRNAs) are short, noncoding RNAs that modulate genes posttranscriptionally. Frequent gains and losses of miRNA genes have been reported to occur during evolution. However, little is known systematically about the periods of evolutionary origin of the present miRNA gene repertoire of an extant mammalian species. Thus, in this study, we estimated the evolutionary periods during which each of 1,433 present human miRNA genes originated within 15 periods, from human to platypus-human common ancestral branch and a class "conserved beyond theria," primarily using multiple genome alignments of 38 species, plus the pairwise genome alignments of five species. The results showed two peak periods in which the human miRNA genes originated at significantly accelerated rates. The most accelerated rate appeared in the period of the initial phase of hominoid lineage, and the second appeared shortly before Laurasiatherian divergence. Approximately 53% of the present human miRNA genes have originated within the simian lineage to human. In particular, approximately 28% originated within the hominoid lineage. The early phase of placental mammal radiation comprises approximately 28%, while no more than 15% of human miRNAs have been conserved beyond placental mammals. We also clearly showed a general trend, in which the miRNA expression level decreases as the miRNA becomes younger. Intriguingly, amid this decreasing trend of expression, we found one significant rise in the expression level that corresponded to the initial phase of the hominoid lineage, suggesting that increased functional acquisitions of miRNAs originated at this particular period. PMID:23171859

  1. The molecular clock of neutral evolution can be accelerated or slowed by asymmetric spatial structure.

    PubMed

    Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C; Paoletti, Christopher; Nowak, Martin A

    2015-02-01

    Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a "molecular clock" to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

  2. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

    PubMed Central

    Currin, Andrew; Swainston, Neil; Day, Philip J.

    2015-01-01

    The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the ‘search space’ of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (K d) and catalytic (k cat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving k cat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the ‘best’ amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole

  3. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.

    PubMed

    Currin, Andrew; Swainston, Neil; Day, Philip J; Kell, Douglas B

    2015-03-01

    The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this

  4. Is the Size Evolution of Massive Galaxies Accelerated in Cluster Environments?

    NASA Astrophysics Data System (ADS)

    Wilson, Gillian

    2013-10-01

    At z 1.6 the main progenitors of present-day massive clusters are undergoing rapid collapse, and have the highest rates of galaxy merging and assembly. Recent observational studies have hinted at accelerated galaxy evolution in dense environments at this epoch, including increased merger rates and rapid growth in galaxy size relative to the field. We propose WFC3 G102 spectroscopy and F125W {Broad J} imaging of a sample of four massive spectroscopically-confirmed clusters at z = 1.6. Our primary scientific goal is to leverage the CANDELS Wide Legacy dataset to carry out a head-to-head comparison of the sizes of cluster members relative to the field {as a function of stellar mass and Sersic index}, and quantify the role of environment in the observed rapid evolution in galaxy sizes since z = 2. These clusters are four of the highest significance overdensities in the 50 square degree SWIRE fields, and will evolve over time to have present-day masses similar to Coma. They were detected using IRAC [3.6]-[4.5] color, which identifies galaxy overdensities regardless of optically red or blue color. A heroic ground-based spectroscopic campaign has resulted in 44 spectroscopically-confirmed members. However this sample is heavily biased toward star-forming {SF} galaxies, and WFC3 spectroscopy is essential to definitively determine cluster membership for 200 members, without bias with respect to quiescent or SF type. The F125W {rest-frame V-band} imaging is necessary to measure the sizes and morphologies of cluster members. 17-passband broadband imaging spanning UV, optical, near-IR, Spitzer IR and Herschel far-IR is already in hand.

  5. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins

    PubMed Central

    Hsiao, Yun-Hua Esther; Bahn, Jae Hoon; Lin, Xianzhi; Chan, Tak-Ming; Wang, Rena; Xiao, Xinshu

    2016-01-01

    Identification of functional genetic variants and elucidation of their regulatory mechanisms represent significant challenges of the post-genomic era. A poorly understood topic is the involvement of genetic variants in mediating post-transcriptional RNA processing, including alternative splicing. Thus far, little is known about the genomic, evolutionary, and regulatory features of genetically modulated alternative splicing (GMAS). Here, we systematically identified intronic tag variants for genetic modulation of alternative splicing using RNA-seq data specific to cellular compartments. Combined with our previous method that identifies exonic tags for GMAS, this study yielded 622 GMAS exons. We observed that GMAS events are highly cell type independent, indicating that splicing-altering genetic variants could have widespread function across cell types. Interestingly, GMAS genes, exons, and single-nucleotide variants (SNVs) all demonstrated positive selection or accelerated evolution in primates. We predicted that GMAS SNVs often alter binding of splicing factors, with SRSF1 affecting the most GMAS events and demonstrating global allelic binding bias. However, in contrast to their GMAS targets, the predicted splicing factors are more conserved than expected, suggesting that cis-regulatory variation is the major driving force of splicing evolution. Moreover, GMAS-related splicing factors had stronger consensus motifs than expected, consistent with their susceptibility to SNV disruption. Intriguingly, GMAS SNVs in general do not alter the strongest consensus position of the splicing factor motif, except the more than 100 GMAS SNVs in linkage disequilibrium with polymorphisms reported by genome-wide association studies. Our study reports many GMAS events and enables a better understanding of the evolutionary and regulatory features of this phenomenon. PMID:26888265

  6. A novel satellite DNA sequence in the Peromyscus genome (PMSat): Evolution via copy number fluctuation.

    PubMed

    Louzada, Sandra; Vieira-da-Silva, Ana; Mendes-da-Silva, Ana; Kubickova, Svatava; Rubes, Jiri; Adega, Filomena; Chaves, Raquel

    2015-11-01

    Satellite DNAs (satDNA) are tandemly arrayed repeated sequences largely present in eukaryotic genomes, which play important roles in genome evolution and function, and therefore, their analysis is vital. Here, we describe the isolation of a novel satellite DNA family (PMSat) from the rodent Peromyscus eremicus (Cricetidae, Rodentia), which is located in pericentromeric regions and exhibits a typical satellite DNA genome organization. Orthologous PMSat sequences were isolated and characterized from three species belonging to Cricetidae: Cricetus cricetus, Phodopus sungorus and Microtus arvalis. In these species, PMSat is highly conserved, with the absence of fixed species-specific mutations. Strikingly, different numbers of copies of this sequence were found among the species, suggesting evolution by copy number fluctuation. Repeat units of PMSat were also found in the Peromyscus maniculatus bairdii BioProject, but our results suggest that these repeat units are from genome regions outside the pericentromere. The remarkably high evolutionary sequence conservation along with the preservation of a few numbers of copies of this sequence in the analyzed genomes may suggest functional significance but a different sequence nature/organization. Our data highlight that repeats are difficult to analyze due to the limited tools available to dissect genomes and the fact that assemblies do not cover regions of constitutive heterochromatin.

  7. Evolution and detectability of comet clouds during post-main-sequence stellar evolution

    NASA Technical Reports Server (NTRS)

    Stern, S. Alan; Brandt, John C.; Shull, J. Michael

    1990-01-01

    The destruction of volatile-rich comet disks and Oort-type clouds around luminous post-main-sequence stars is modeled. The models are in agreement with several aspects of existing observations of water and complex molecules in the envelopes of giant and supergiant stars. If confirmed, these results would establish the common existence of Oort-type clouds around other stars and would constitute indirect evidence for sites of past planetary formation.

  8. Metabolic acceleration and the evolution of human brain size and life history.

    PubMed

    Pontzer, Herman; Brown, Mary H; Raichlen, David A; Dunsworth, Holly; Hare, Brian; Walker, Kara; Luke, Amy; Dugas, Lara R; Durazo-Arvizu, Ramon; Schoeller, Dale; Plange-Rhule, Jacob; Bovet, Pascal; Forrester, Terrence E; Lambert, Estelle V; Thompson, Melissa Emery; Shumaker, Robert W; Ross, Stephen R

    2016-05-19

    Humans are distinguished from the other living apes in having larger brains and an unusual life history that combines high reproductive output with slow childhood growth and exceptional longevity. This suite of derived traits suggests major changes in energy expenditure and allocation in the human lineage, but direct measures of human and ape metabolism are needed to compare evolved energy strategies among hominoids. Here we used doubly labelled water measurements of total energy expenditure (TEE; kcal day(-1)) in humans, chimpanzees, bonobos, gorillas and orangutans to test the hypothesis that the human lineage has experienced an acceleration in metabolic rate, providing energy for larger brains and faster reproduction without sacrificing maintenance and longevity. In multivariate regressions including body size and physical activity, human TEE exceeded that of chimpanzees and bonobos, gorillas and orangutans by approximately 400, 635 and 820 kcal day(-1), respectively, readily accommodating the cost of humans' greater brain size and reproductive output. Much of the increase in TEE is attributable to humans' greater basal metabolic rate (kcal day(-1)), indicating increased organ metabolic activity. Humans also had the greatest body fat percentage. An increased metabolic rate, along with changes in energy allocation, was crucial in the evolution of human brain size and life history. PMID:27144364

  9. Evolution of the solar wind acceleration region during 1990-1994

    NASA Technical Reports Server (NTRS)

    Tokumaru, M.; Kondo, T.; Takaba, H.; Mori, H.; Tanaka, T.

    1995-01-01

    The single-station measurements of interplanetary scintillation (IPS) at 2 and 8 GHz have been made at the Kashima Space Research Center of the Communications Research Laboratory in the period from 1990 to 1994. These IPS data are used to study the radial distribution of solar wind velocity and density fluctuations near the sun (i.e. 10-70 Rs), and the long-term variation in these properties. The IPS co-spectrum technique is applied here to estimate the solar wind velocity. Derived velocities show that the solar wind gains a speed significantly in the radial range from 10 to 30 Rs (solar radii). which is much farther than the source surface of the thermally driven solar wind model. From the scintillation index analysis. it is found that the radial fall of density fluctuations is well described by the power-law function. A series of IPS observations reveals that a pronounced change in velocity and turbulence level for this radial range occurs at the polar region of the sun during 1990-1994. That is, the high speed wind and the reduced turbulence region develop there as the solar activity declines. On the other hand, little long-term variation is observed for the solar wind acceleration region at a low latitude. From the comparison with He 1O83 nm observations. it is demonstrated that the change of the solar wind structure is closely linked with the evolution of the coronal hole on the solar surface.

  10. Metabolic acceleration and the evolution of human brain size and life history

    PubMed Central

    Pontzer, Herman; Brown, Mary H.; Raichlen, David A.; Dunsworth, Holly; Hare, Brian; Walker, Kara; Luke, Amy; Dugas, Lara R.; Durazo-Arvizu, Ramon; Schoeller, Dale; Plange-Rhule, Jacob; Bovet, Pascal; Forrester, Terrence E.; Lambert, Estelle V.; Thompson, Melissa Emery; Shumaker, Robert W.; Ross, Stephen R.

    2016-01-01

    Humans are distinguished from the other living apes in having larger brains and an unusual life history that combines high reproductive output with slow childhood growth and exceptional longevity1. This suite of derived traits suggests major changes in energy expenditure and allocation in the human lineage, but direct measures of human and ape metabolism are needed to compare evolved energy strategies among hominoids. Here we used doubly labelled water measurements of total energy expenditure (TEE; kcal day−1) in humans, chimpanzees, bonobos, gorillas and orangutans to test the hypothesis that the human lineage has experienced an acceleration in metabolic rate, providing energy for larger brains and faster reproduction without sacrificing maintenance and longevity. In multivariate regressions including body size and physical activity, human TEE exceeded that of chimpanzees and bonobos, gorillas and orangutans by approximately 400, 635 and 820 kcal day−1, respectively, readily accommodating the cost of humans' greater brain size and reproductive output. Much of the increase in TEE is attributable to humans' greater basal metabolic rate (kcal day−1), indicating increased organ metabolic activity. Humans also had the greatest body fat percentage. An increased metabolic rate, along with changes in energy allocation, was crucial in the evolution of human brain size and life history. PMID:27144364

  11. Evolution in Fast Forward: a Potential Role for Mutators in Accelerating Staphylococcus aureus Pathoadaptation

    PubMed Central

    Canfield, Gregory S.; Schwingel, Johanna M.; Foley, Matthew H.; Vore, Kelly L.; Boonanantanasarn, Kanitsak; Gill, Ann L.; Sutton, Mark D.

    2013-01-01

    Pathogen evolution and subsequent phenotypic heterogeneity during chronic infection are proposed to enhance Staphylococcus aureus survival during human infection. We tested this theory by genetically and phenotypically characterizing strains with mutations constructed in the mismatch repair (MMR) and oxidized guanine (GO) system, termed mutators, which exhibit increased spontaneous-mutation frequencies. Analysis of these mutators revealed not only strain-dependent increases in the spontaneous-mutation frequency but also shifts in mutational type and hot spots consistent with loss of GO or MMR functions. Although the GO and MMR systems are relied upon in some bacterial species to prevent reactive oxygen species-induced DNA damage, no deficit in hydrogen peroxide sensitivity was found when either of these DNA repair pathways was lost in S. aureus. To gain insight into the contribution of increased mutation supply to S. aureus pathoadaptation, we measured the rate of α-hemolysin and staphyloxanthin inactivation during serial passage. Detection of increased rates of α-hemolysin and staphyloxanthin inactivation in GO and MMR mutants suggests that these strains are capable of modifying virulence phenotypes implicated in mediating infection. Accelerated derivation of altered virulence phenotypes, combined with the absence of increased ROS sensitivity, highlights the potential of mutators to drive pathoadaptation in the host and serve as catalysts for persistent infections. PMID:23204459

  12. Metabolic acceleration and the evolution of human brain size and life history.

    PubMed

    Pontzer, Herman; Brown, Mary H; Raichlen, David A; Dunsworth, Holly; Hare, Brian; Walker, Kara; Luke, Amy; Dugas, Lara R; Durazo-Arvizu, Ramon; Schoeller, Dale; Plange-Rhule, Jacob; Bovet, Pascal; Forrester, Terrence E; Lambert, Estelle V; Thompson, Melissa Emery; Shumaker, Robert W; Ross, Stephen R

    2016-05-04

    Humans are distinguished from the other living apes in having larger brains and an unusual life history that combines high reproductive output with slow childhood growth and exceptional longevity. This suite of derived traits suggests major changes in energy expenditure and allocation in the human lineage, but direct measures of human and ape metabolism are needed to compare evolved energy strategies among hominoids. Here we used doubly labelled water measurements of total energy expenditure (TEE; kcal day(-1)) in humans, chimpanzees, bonobos, gorillas and orangutans to test the hypothesis that the human lineage has experienced an acceleration in metabolic rate, providing energy for larger brains and faster reproduction without sacrificing maintenance and longevity. In multivariate regressions including body size and physical activity, human TEE exceeded that of chimpanzees and bonobos, gorillas and orangutans by approximately 400, 635 and 820 kcal day(-1), respectively, readily accommodating the cost of humans' greater brain size and reproductive output. Much of the increase in TEE is attributable to humans' greater basal metabolic rate (kcal day(-1)), indicating increased organ metabolic activity. Humans also had the greatest body fat percentage. An increased metabolic rate, along with changes in energy allocation, was crucial in the evolution of human brain size and life history.

  13. Pleiotropic constraints, expression level, and the evolution of miRNA sequences.

    PubMed

    Jovelin, Richard

    2013-12-01

    Post-transcriptional gene regulation mediated by microRNAs (miRNAs) plays critical roles during development by modulating gene expression and conferring robustness to stochastic errors. Phylogenetic analyses suggest that miRNA acquisition could play a role in phenotypic innovation. Moreover, miRNA-induced regulation strongly impacts genome evolution, increasing selective constraints on 3'UTRs, protein sequences, and expression level divergence. Thus, it is essential to understand the factors governing sequence evolution for this important class of regulatory molecules. Investigation of the patterns of molecular evolution at miRNA loci have been limited in Caenorhabditis elegans because of the lack of a close outgroup. Instead, I used Caenorhabditis briggsae as the focus point of this study because of its close relationship to Caenorhabditis sp. 9. I also corroborated the patterns of sequence evolution in Caenorhabditis using published orthologous relationships among miRNAs in Drosophila. In nematodes and in flies, miRNA sequence divergence is not influenced by the genomic neighborhood (i.e., intronic or intergenic) but is nevertheless affected by the genomic context because X-linked miRNAs evolve faster than autosomal miRNAs. However, this effect of chromosomal linkage can be explained by differential expression levels rather than a fast-X effect. The results presented here support a universal negative relationship between rates of molecular evolution and expression level, and suggest that mutations in highly expressed miRNAs are more likely to be deleterious because they potentially affect a larger number of target genes. Finally, I show that many single family member miRNAs evolve faster than miRNAs from multigene families and have limited functional scope, suggesting that they are not strongly integrated in gene regulatory networks.

  14. Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software.

    PubMed

    Nakano, Shogo; Asano, Yasuhisa

    2015-02-03

    Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.

  15. Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software

    PubMed Central

    Nakano, Shogo; Asano, Yasuhisa

    2015-01-01

    Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs. PMID:25645341

  16. Modeling the expected lifetime and evolution of a deme's principal genetic sequence.

    NASA Astrophysics Data System (ADS)

    Clark, Brian

    2014-03-01

    The principal genetic sequence (PGS) is the most common genetic sequence in a deme. The PGS changes over time because new genetic sequences are created by inversions, compete with the current PGS, and a small fraction become PGSs. A set of coupled difference equations provides a description of the evolution of the PGS distribution function in an ensemble of demes. Solving the set of equations produces the survival probability of a new genetic sequence and the expected lifetime of an existing PGS as a function of inversion size and rate, recombination rate, and deme size. Additionally, the PGS distribution function is used to explain the transition pathway from old to new PGSs. We compare these results to a cellular automaton based representation of a deme and the drosophila species, D. melanogaster and D. yakuba.

  17. New insights about enzyme evolution from large scale studies of sequence and structure relationships.

    PubMed

    Brown, Shoshana D; Babbitt, Patricia C

    2014-10-31

    Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes.

  18. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

    PubMed Central

    2008-01-01

    Background Accurately modeling the sequence substitution process is required for the correct estimation of evolutionary parameters, be they phylogenetic relationships, substitution rates or ancestral states; it is also crucial to simulate realistic data sets. Such simulation procedures are needed to estimate the null-distribution of complex statistics, an approach referred to as parametric bootstrapping, and are also used to test the quality of phylogenetic reconstruction programs. It has often been observed that homologous sequences can vary widely in their nucleotide or amino-acid compositions, revealing that sequence evolution has changed importantly among lineages, and may therefore be most appropriately approached through non-homogeneous models. Several programs implementing such models have been developed, but they are limited in their possibilities: only a few particular models are available for likelihood optimization, and data sets cannot be easily generated using the resulting estimated parameters. Results We hereby present a general implementation of non-homogeneous models of substitutions. It is available as dedicated classes in the Bio++ libraries and can hence be used in any C++ program. Two programs that use these classes are also presented. The first one, Bio++ Maximum Likelihood (BppML), estimates parameters of any non-homogeneous model and the second one, Bio++ Sequence Generator (BppSeqGen), simulates the evolution of sequences from these models. These programs allow the user to describe non-homogeneous models through a property file with a simple yet powerful syntax, without any programming required. Conclusion We show that the general implementation introduced here can accommodate virtually any type of non-homogeneous models of sequence evolution, including heterotachous ones, while being computer efficient. We furthermore illustrate the use of such general models for parametric bootstrapping, using tests of non-homogeneity applied to an

  19. Genome sequence diversity and clues to the evolution of variola (smallpox) virus.

    PubMed

    Esposito, Joseph J; Sammons, Scott A; Frace, A Michael; Osborne, John D; Olsen-Rasmussen, Melissa; Zhang, Ming; Govil, Dhwani; Damon, Inger K; Kline, Richard; Laker, Miriam; Li, Yu; Smith, Geoffrey L; Meyer, Hermann; Leduc, James W; Wohlhueter, Robert M

    2006-08-11

    Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the latter implicated putative proteins that mediate viral virulence differences. Analysis of the viral linear DNA genome suggests that its evolution involved direct descent and DNA end-region recombination events. Knowing the sequences will help understand the viral proteome and improve diagnostic test precision, therapeutics, and systems for their assessment.

  20. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea.

    PubMed

    Tran, Trung D; Cao, Hieu X; Jovtchev, Gabriele; Neumann, Pavel; Novák, Petr; Fojtová, Miloslava; Vu, Giang T H; Macas, Jiří; Fajkus, Jiří; Schubert, Ingo; Fuchs, Joerg

    2015-12-01

    Linear chromosomes of eukaryotic organisms invariably possess centromeres and telomeres to ensure proper chromosome segregation during nuclear divisions and to protect the chromosome ends from deterioration and fusion, respectively. While centromeric sequences may differ between species, with arrays of tandemly repeated sequences and retrotransposons being the most abundant sequence types in plant centromeres, telomeric sequences are usually highly conserved among plants and other organisms. The genome size of the carnivorous genus Genlisea (Lentibulariaceae) is highly variable. Here we study evolutionary sequence plasticity of these chromosomal domains at an intrageneric level. We show that Genlisea nigrocaulis (1C = 86 Mbp; 2n = 40) and G. hispidula (1C = 1550 Mbp; 2n = 40) differ as to their DNA composition at centromeres and telomeres. G. nigrocaulis and its close relative G. pygmaea revealed mainly 161 bp tandem repeats, while G. hispidula and its close relative G. subglabra displayed a combination of four retroelements at centromeric positions. G. nigrocaulis and G. pygmaea chromosome ends are characterized by the Arabidopsis-type telomeric repeats (TTTAGGG); G. hispidula and G. subglabra instead revealed two intermingled sequence variants (TTCAGG and TTTCAGG). These differences in centromeric and, surprisingly, also in telomeric DNA sequences, uncovered between groups with on average a > 9-fold genome size difference, emphasize the fast genome evolution within this genus. Such intrageneric evolutionary alteration of telomeric repeats with cytosine in the guanine-rich strand, not yet known for plants, might impact the epigenetic telomere chromatin modification.

  1. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea.

    PubMed

    Tran, Trung D; Cao, Hieu X; Jovtchev, Gabriele; Neumann, Pavel; Novák, Petr; Fojtová, Miloslava; Vu, Giang T H; Macas, Jiří; Fajkus, Jiří; Schubert, Ingo; Fuchs, Joerg

    2015-12-01

    Linear chromosomes of eukaryotic organisms invariably possess centromeres and telomeres to ensure proper chromosome segregation during nuclear divisions and to protect the chromosome ends from deterioration and fusion, respectively. While centromeric sequences may differ between species, with arrays of tandemly repeated sequences and retrotransposons being the most abundant sequence types in plant centromeres, telomeric sequences are usually highly conserved among plants and other organisms. The genome size of the carnivorous genus Genlisea (Lentibulariaceae) is highly variable. Here we study evolutionary sequence plasticity of these chromosomal domains at an intrageneric level. We show that Genlisea nigrocaulis (1C = 86 Mbp; 2n = 40) and G. hispidula (1C = 1550 Mbp; 2n = 40) differ as to their DNA composition at centromeres and telomeres. G. nigrocaulis and its close relative G. pygmaea revealed mainly 161 bp tandem repeats, while G. hispidula and its close relative G. subglabra displayed a combination of four retroelements at centromeric positions. G. nigrocaulis and G. pygmaea chromosome ends are characterized by the Arabidopsis-type telomeric repeats (TTTAGGG); G. hispidula and G. subglabra instead revealed two intermingled sequence variants (TTCAGG and TTTCAGG). These differences in centromeric and, surprisingly, also in telomeric DNA sequences, uncovered between groups with on average a > 9-fold genome size difference, emphasize the fast genome evolution within this genus. Such intrageneric evolutionary alteration of telomeric repeats with cytosine in the guanine-rich strand, not yet known for plants, might impact the epigenetic telomere chromatin modification. PMID:26485466

  2. Sequence and evolution of HLA-DR7- and -DRw53-associated beta-chain genes.

    PubMed

    Young, J A; Wilkinson, D; Bodmer, W F; Trowsdale, J

    1987-07-01

    cDNA clones representing products of the DR7 and DRw53 beta-chain genes were isolated from the human B-lymphoblastoid cell line MANN (DR7,DRw53,DQw2, DPw2). The DRw53 beta sequence was identical to a DRw53 beta sequence derived from cells with a DR4 haplotype. In contrast, the DR7 beta sequence was as unrelated to DR4 beta sequence as it was to other DR beta-related genes, except at the 3'-untranslated region. These results suggest that the DR7 and DR4 haplotypes may have been derived relatively recently from a common ancestral haplotype and that the DR4 and DR7 beta-chain genes have undergone more rapid diversification in their beta 1 domains, most probably as a result of natural selection, than have the DRw53 beta-chain genes. Short tracts of sequence within the DR7 and DRw53 beta 1 domains were shared with other DR beta sequences, indicating that exchanges of genetic information between beta 1 domains of DR beta-related genes have played a part in their evolution. Serological analysis of mouse L-cell transfectants expressing surface HLA-DR7 molecules, confirmed by antibody binding and allelic sequence comparisons, identified amino acid residues that may be critical to the binding of a monomorphic DR- and DP-specific monoclonal antibody.

  3. Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.)

    PubMed Central

    2010-01-01

    Background Obligate biotrophs such as rust fungi are believed to establish long-term relationships by modulating plant defenses through a plethora of effector proteins, whose most recognizable feature is the presence of a signal peptide for secretion. Since the phenotypes of these effectors extend to host cells, their genes are expected to be under accelerated evolution stimulated by host-pathogen coevolutionary arms races. Recently, whole genome sequence data has allowed the prediction of secretomes, facilitating the identification of putative effectors. Results We generated cDNA libraries from four poplar leaf rust pathogens (Melampsora spp.) and used computational approaches to identify and annotate putative secreted proteins with the aim of uncovering new knowledge about the nature and evolution of the rust secretome. While more than half of the predicted secretome members encoded lineage-specific proteins, similarities with experimentally characterized fungal effectors were also identified. A SAGE analysis indicated a strong stage-specific regulation of transcripts encoding secreted proteins. The average sequence identity of putative secreted proteins to their closest orthologs in the wheat stem rust Puccinia graminis f. sp. tritici was dramatically reduced compared with non-secreted ones. A comparative genomics approach based on homologous gene groups unravelled positive selection in putative members of the secretome. Conclusion We uncovered robust evidence that different evolutionary constraints are acting on the rust secretome when compared to the rest of the genome. These results are consistent with the view that these genes are more likely to exhibit an effector activity and be involved in coevolutionary arms races with host factors. PMID:20615251

  4. Morphological evolution of cluster red sequence galaxies in the past 9 Gyr

    NASA Astrophysics Data System (ADS)

    De Propris, Roberto; Bremer, Malcolm N.; Phillipps, Steven

    2016-10-01

    Galaxies arrive on the red sequences of clusters at high redshift (z > 1) once their star formation is quenched and evolve passively thereafter. However, we have previously found that cluster red sequence galaxies (CRSGs) undergo significant morphological evolution subsequent to the cessation of star formation, at some point in the past 9-10 Gyr. Through a detailed study of a large sample of cluster red sequence galaxies spanning 0.2 < z < 1.4 we elucidate the details of this evolution. Below z ˜ 0.5-0.6 (in the last 5-6 Gyr) there is little or no morphological evolution in the population as a whole, unlike in the previous 4-5 Gyr. Over this earlier time (i) disc-like systems with Sérsic n < 2 progressively disappear, as (ii) the range of their axial ratios similarly decreases, removing the most elongated systems (those consistent with thin discs seen at an appreciable inclination angle) and (iii) radial colour gradients (bluer outwards) decrease in an absolute sense from significant age-related gradients to a residual level consistent with the metallicity-induced gradients seen in low-redshift cluster members. The distribution of their effective radii shows some evidence of evolution, consistent with growth of at most a factor <1.5 between z ˜ 1.4 and ˜0.5, significantly less than for comparable field galaxies, while the distribution of their central (<1 kpc) bulge surface densities shows no evolution at least at z < 1. A simple model involving the fading and thickening of a disc component after comparatively recent quenching (after z ˜ 1.5) around an otherwise passively evolving older spheroid component is consistent with all of these findings.

  5. Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont.

    PubMed

    Williams, Laura E; Wernegreen, Jennifer J

    2013-01-01

    Indel mutations play key roles in genome and protein evolution, yet we lack a comprehensive understanding of how indels impact evolutionary processes. Genome-wide analyses enabled by next-generation sequencing can clarify the context and effect of indels, thereby integrating a more detailed consideration of indels with our knowledge of nucleotide substitutions. To this end, we sequenced Blochmannia chromaiodes, an obligate bacterial endosymbiont of carpenter ants, and compared it with the close relative, B. pennsylvanicus. The genetic distance between these species is small enough for accurate whole genome alignment but large enough to provide a meaningful spectrum of indel mutations. We found that indels are subjected to purifying selection in coding regions and even intergenic regions, which show a reduced rate of indel base pairs per kilobase compared with nonfunctional pseudogenes. Indels occur almost exclusively in repeat regions composed of homopolymers and multimeric simple sequence repeats, demonstrating the importance of sequence context for indel mutations. Despite purifying selection, some indels occur in protein-coding genes. Most are multiples of three, indicating selective pressure to maintain the reading frame. The deleterious effect of frameshift-inducing indels is minimized by either compensation from a nearby indel to restore reading frame or the indel's location near the 3'-end of the gene. We observed amino acid divergence exceeding nucleotide divergence in regions affected by frameshift-inducing indels, suggesting that these indels may either drive adaptive protein evolution or initiate gene degradation. Our results shed light on how indel mutations impact processes of molecular evolution underlying endosymbiont genome evolution.

  6. Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont.

    PubMed

    Williams, Laura E; Wernegreen, Jennifer J

    2013-01-01

    Indel mutations play key roles in genome and protein evolution, yet we lack a comprehensive understanding of how indels impact evolutionary processes. Genome-wide analyses enabled by next-generation sequencing can clarify the context and effect of indels, thereby integrating a more detailed consideration of indels with our knowledge of nucleotide substitutions. To this end, we sequenced Blochmannia chromaiodes, an obligate bacterial endosymbiont of carpenter ants, and compared it with the close relative, B. pennsylvanicus. The genetic distance between these species is small enough for accurate whole genome alignment but large enough to provide a meaningful spectrum of indel mutations. We found that indels are subjected to purifying selection in coding regions and even intergenic regions, which show a reduced rate of indel base pairs per kilobase compared with nonfunctional pseudogenes. Indels occur almost exclusively in repeat regions composed of homopolymers and multimeric simple sequence repeats, demonstrating the importance of sequence context for indel mutations. Despite purifying selection, some indels occur in protein-coding genes. Most are multiples of three, indicating selective pressure to maintain the reading frame. The deleterious effect of frameshift-inducing indels is minimized by either compensation from a nearby indel to restore reading frame or the indel's location near the 3'-end of the gene. We observed amino acid divergence exceeding nucleotide divergence in regions affected by frameshift-inducing indels, suggesting that these indels may either drive adaptive protein evolution or initiate gene degradation. Our results shed light on how indel mutations impact processes of molecular evolution underlying endosymbiont genome evolution. PMID:23475937

  7. Accelerating Sequences in the Presence of Metal by Exploiting the Spatial Distribution of Off-Resonance

    PubMed Central

    Smith, Matthew R.; Artz, Nathan S.; Koch, Kevin M.; Samsonov, Alexey; Reeder, Scott B.

    2014-01-01

    Purpose To demonstrate feasibility of exploiting the spatial distribution of off-resonance surrounding metallic implants for accelerating multispectral imaging techniques. Theory Multispectral imaging (MSI) techniques perform time-consuming independent 3D acquisitions with varying RF frequency offsets to address the extreme off-resonance from metallic implants. Each off-resonance bin provides a unique spatial sensitivity that is analogous to the sensitivity of a receiver coil, and therefore provides a unique opportunity for acceleration. Methods Fully sampled MSI was performed to demonstrate retrospective acceleration. A uniform sampling pattern across off-resonance bins was compared to several adaptive sampling strategies using a total hip replacement phantom. Monte Carlo simulations were performed to compare noise propagation of two of these strategies. With a total knee replacement phantom, positive and negative off-resonance bins were strategically sampled with respect to the B0 field to minimize aliasing. Reconstructions were performed with a parallel imaging framework to demonstrate retrospective acceleration. Results An adaptive sampling scheme dramatically improved reconstruction quality, which was supported by the noise propagation analysis. Independent acceleration of negative and positive off-resonance bins demonstrated reduced overlapping of aliased signal to improve the reconstruction. Conclusion This work presents the feasibility of acceleration in the presence of metal by exploiting the spatial sensitivities of off-resonance bins. PMID:24431210

  8. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

    PubMed Central

    Kim, Kyunghee; Lee, Sang-Choon; Lee, Junki; Yu, Yeisoo; Yang, Kiwoung; Choi, Beom-Soon; Koh, Hee-Jong; Waminal, Nomar Espinosa; Choi, Hong-Il; Kim, Nam-Hoon; Jang, Woojong; Park, Hyun-Seung; Lee, Jonghoon; Lee, Hyun Oh; Joh, Ho Jun; Lee, Hyeon Ju; Park, Jee Young; Perumal, Sampath; Jayakodi, Murukarthick; Lee, Yun Sun; Kim, Backki; Copetti, Dario; Kim, Soonok; Kim, Sunggil; Lim, Ki-Byung; Kim, Young-Dong; Lee, Jungho; Cho, Kwang-Su; Park, Beom-Seok; Wing, Rod A.; Yang, Tae-Jin

    2015-01-01

    Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis. PMID:26506948

  9. Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees.

    PubMed

    Jasper, William Cameron; Linksvayer, Timothy A; Atallah, Joel; Friedman, Daniel; Chiu, Joanna C; Johnson, Brian R

    2015-02-01

    Whether coding or regulatory sequence change is more important to the evolution of phenotypic novelty is one of biology's major unresolved questions. The field of evo-devo has shown that in early development changes to regulatory regions are the dominant mode of genetic change, but whether this extends to the evolution of novel phenotypes in the adult organism is unclear. Here, we conduct ten RNA-Seq experiments across both novel and conserved tissues in the honey bee to determine to what extent postdevelopmental novelty is based on changes to the coding regions of genes. We make several discoveries. First, we show that with respect to novel physiological functions in the adult animal, positively selected tissue-specific genes of high expression underlie novelty by conferring specialized cellular functions. Such genes are often, but not always taxonomically restricted genes (TRGs). We further show that positively selected genes, whether TRGs or conserved genes, are the least connected genes within gene expression networks. Overall, this work suggests that the evo-devo paradigm is limited, and that the evolution of novelty, postdevelopment, follows additional rules. Specifically, evo-devo stresses that high network connectedness (repeated use of the same gene in many contexts) constrains coding sequence change as it would lead to negative pleiotropic effects. Here, we show that in the adult animal, the converse is true: Genes with low network connectedness (TRGs and tissue-specific conserved genes) underlie novel phenotypes by rapidly changing coding sequence to perform new-specialized functions. PMID:25351750

  10. Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees.

    PubMed

    Jasper, William Cameron; Linksvayer, Timothy A; Atallah, Joel; Friedman, Daniel; Chiu, Joanna C; Johnson, Brian R

    2015-02-01

    Whether coding or regulatory sequence change is more important to the evolution of phenotypic novelty is one of biology's major unresolved questions. The field of evo-devo has shown that in early development changes to regulatory regions are the dominant mode of genetic change, but whether this extends to the evolution of novel phenotypes in the adult organism is unclear. Here, we conduct ten RNA-Seq experiments across both novel and conserved tissues in the honey bee to determine to what extent postdevelopmental novelty is based on changes to the coding regions of genes. We make several discoveries. First, we show that with respect to novel physiological functions in the adult animal, positively selected tissue-specific genes of high expression underlie novelty by conferring specialized cellular functions. Such genes are often, but not always taxonomically restricted genes (TRGs). We further show that positively selected genes, whether TRGs or conserved genes, are the least connected genes within gene expression networks. Overall, this work suggests that the evo-devo paradigm is limited, and that the evolution of novelty, postdevelopment, follows additional rules. Specifically, evo-devo stresses that high network connectedness (repeated use of the same gene in many contexts) constrains coding sequence change as it would lead to negative pleiotropic effects. Here, we show that in the adult animal, the converse is true: Genes with low network connectedness (TRGs and tissue-specific conserved genes) underlie novel phenotypes by rapidly changing coding sequence to perform new-specialized functions.

  11. Evolution of Wake Instabilities and the Acceleration of the Slow Solar Wind: Melon Seed and Expansion Effects

    NASA Astrophysics Data System (ADS)

    Rappazzo, A. F.; Velli, M.; Einaudi, G.; Dahlburg, R. B.

    2003-09-01

    We extend previous 2D simulation studies of slow solar wind acceleration due to the nonlinear evolution of the instability of the plasma/current sheet above streamers. We include the effects of the melon-seed force due to the overall magnetic field radial gradients on the plasmoid formed by the instability, as well as the subsequent expansion effects using the Expanding Box Model.

  12. Massive Thermal Acceleration of the Emergence of Primordial Chemistry, the Incidence of Spontaneous Mutation, and the Evolution of Enzymes*

    PubMed Central

    Wolfenden, Richard

    2014-01-01

    Kelvin considered it unlikely that sufficient time had elapsed on the earth for life to have reached its present level of complexity. In the warm surroundings in which life first appeared, however, elevated temperatures would have reduced the kinetic barriers to reaction. Recent experiments disclose the profound extent to which very slow reactions are accelerated by elevated temperatures, collapsing the time that would have been required for early events in primordial chemistry before the advent of enzymes. If a primitive enzyme, like model catalysts and most modern enzymes, accelerated a reaction by lowering its enthalpy of activation, then the rate enhancement that it produced would have increased automatically as the environment cooled, quite apart from any improvements in catalytic activity that arose from mutation and natural selection. The chemical events responsible for spontaneous mutation are also highly sensitive to temperature, furnishing an independent mechanism for accelerating evolution. PMID:25210030

  13. Massive thermal acceleration of the emergence of primordial chemistry, the incidence of spontaneous mutation, and the evolution of enzymes.

    PubMed

    Wolfenden, Richard

    2014-10-31

    Kelvin considered it unlikely that sufficient time had elapsed on the earth for life to have reached its present level of complexity. In the warm surroundings in which life first appeared, however, elevated temperatures would have reduced the kinetic barriers to reaction. Recent experiments disclose the profound extent to which very slow reactions are accelerated by elevated temperatures, collapsing the time that would have been required for early events in primordial chemistry before the advent of enzymes. If a primitive enzyme, like model catalysts and most modern enzymes, accelerated a reaction by lowering its enthalpy of activation, then the rate enhancement that it produced would have increased automatically as the environment cooled, quite apart from any improvements in catalytic activity that arose from mutation and natural selection. The chemical events responsible for spontaneous mutation are also highly sensitive to temperature, furnishing an independent mechanism for accelerating evolution.

  14. Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

    PubMed

    Kijima, T E; Innan, Hideki

    2013-11-01

    A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

  15. Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences

    PubMed Central

    Bentley, Stephen D

    2014-01-01

    Evolution of bacterial pathogen populations has been detected in a variety of ways including phenotypic tests, such as metabolic activity, reaction to antisera and drug resistance and genotypic tests that measure variation in chromosome structure, repetitive loci and individual gene sequences. While informative, these methods only capture a small subset of the total variation and, therefore, have limited resolution. Advances in sequencing technologies have made it feasible to capture whole-genome sequence variation for each sample under study, providing the potential to detect all changes at all positions in the genome from single nucleotide changes to large-scale insertions and deletions. In this review, we focus on recent work that has applied this powerful new approach and summarize some of the advances that this has brought in our understanding of the details of how bacterial pathogens evolve. PMID:23075447

  16. Empirical analysis of RNA robustness and evolution using high-throughput sequencing of ribozyme reactions.

    PubMed

    Hayden, Eric J

    2016-08-15

    RNA molecules provide a realistic but tractable model of a genotype to phenotype relationship. This relationship has been extensively investigated computationally using secondary structure prediction algorithms. Enzymatic RNA molecules, or ribozymes, offer access to genotypic and phenotypic information in the laboratory. Advancements in high-throughput sequencing technologies have enabled the analysis of sequences in the lab that now rivals what can be accomplished computationally. This has motivated a resurgence of in vitro selection experiments and opened new doors for the analysis of the distribution of RNA functions in genotype space. A body of computational experiments has investigated the persistence of specific RNA structures despite changes in the primary sequence, and how this mutational robustness can promote adaptations. This article summarizes recent approaches that were designed to investigate the role of mutational robustness during the evolution of RNA molecules in the laboratory, and presents theoretical motivations, experimental methods and approaches to data analysis. PMID:27215494

  17. Systematic Analysis of Long Noncoding RNAs in the Senescence-accelerated Mouse Prone 8 Brain Using RNA Sequencing.

    PubMed

    Zhang, Shuai; Qin, Chunxia; Cao, Guoqiong; Xin, Wenfeng; Feng, Chengqiang; Zhang, Wensheng

    2016-01-01

    Long noncoding RNAs (lncRNAs) may play an important role in Alzheimer's disease (AD) pathogenesis. However, despite considerable research in this area, the comprehensive and systematic understanding of lncRNAs in AD is still limited. The emergence of RNA sequencing provides a predictor and has incomparable advantage compared with other methods, including microarray. In this study, we identified lncRNAs in a 7-month-old mouse brain through deep RNA sequencing using the senescence-accelerated mouse prone 8 (SAMP8) and senescence-accelerated mouse resistant 1 (SAMR1) models. A total of 599,985,802 clean reads and 23,334 lncRNA transcripts were obtained. Then, we identified 97 significantly upregulated and 114 significantly downregulated lncRNA transcripts from all cases in SAMP8 mice relative to SAMR1 mice. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these significantly dysregulated lncRNAs were involved in regulating the development of AD from various angles, such as nerve growth factor term (GO: 1990089), mitogen-activated protein kinase signaling pathway, and AD pathway. Furthermore, the most probable AD-associated lncRNAs were predicted and listed in detail. Our study provided the systematic dissection of lncRNA profiling in SAMP8 mouse brain and accelerated the development of lncRNA biomarkers in AD. These attracting biomarkers could provide significant insights into AD therapy in the future. PMID:27483026

  18. Systematic Analysis of Long Noncoding RNAs in the Senescence-accelerated Mouse Prone 8 Brain Using RNA Sequencing

    PubMed Central

    Zhang, Shuai; Qin, Chunxia; Cao, Guoqiong; Xin, Wenfeng; Feng, Chengqiang; Zhang, Wensheng

    2016-01-01

    Long noncoding RNAs (lncRNAs) may play an important role in Alzheimer's disease (AD) pathogenesis. However, despite considerable research in this area, the comprehensive and systematic understanding of lncRNAs in AD is still limited. The emergence of RNA sequencing provides a predictor and has incomparable advantage compared with other methods, including microarray. In this study, we identified lncRNAs in a 7-month-old mouse brain through deep RNA sequencing using the senescence-accelerated mouse prone 8 (SAMP8) and senescence-accelerated mouse resistant 1 (SAMR1) models. A total of 599,985,802 clean reads and 23,334 lncRNA transcripts were obtained. Then, we identified 97 significantly upregulated and 114 significantly downregulated lncRNA transcripts from all cases in SAMP8 mice relative to SAMR1 mice. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these significantly dysregulated lncRNAs were involved in regulating the development of AD from various angles, such as nerve growth factor term (GO: 1990089), mitogen-activated protein kinase signaling pathway, and AD pathway. Furthermore, the most probable AD-associated lncRNAs were predicted and listed in detail. Our study provided the systematic dissection of lncRNA profiling in SAMP8 mouse brain and accelerated the development of lncRNA biomarkers in AD. These attracting biomarkers could provide significant insights into AD therapy in the future. PMID:27483026

  19. Temporal Development of Auroral Acceleration Potentials: High-Altitude Evolutionary Sequences, Drivers and Consequences

    NASA Astrophysics Data System (ADS)

    Hull, A. J.; Wilber, M.; Chaston, C.; Bonnell, J.; Mozer, F.; McFadden, J.; Goldstein, M.; Fillingim, M.

    2007-12-01

    The region above the auroral acceleration region is an integral part of the auroral zone electrodynamic system. At these altitudes (≥ 3 Re) we find the source plasma and fields that determine acceleration processes occurring at lower altitudes, which play a key role in the transport of mass and energy into the ionosphere. Dynamic changes in these high-altitude regions can affect and/or control lower-altitude acceleration processes according to how field-aligned currents and specific plasma sources form and decay and how they are spatially distributed, and through magnetic configuration changes deeper in the magnetotail. Though much progress has been made, the time development and consequential effects of the high-altitude plasma and fields are still not fully understood. We present Cluster multi-point observations at key instances within and above the acceleration region (> 3 RE) of evolving auroral arc current systems. Results are presented from events occurring under different conditions, such as magnetospheric activity, associations with density depletions or gradients, and Alfvenic turbulence. A preliminary survey, primarily at or near the plasma sheet boundary, indicates quasi- static up-down current pair systems are at times associated with density depletions and other instances occur in association with density gradients. The data suggest that such quasi-static current systems may be evolving from structured Alfvenic current systems. We will discuss the temporal development of auroral acceleration potentials, plasma and currents, including quasi-static system formation from turbulent systems of structured Alfvenic field-aligned currents, density depletion and constituent reorganization of the source and ionospheric plasma that transpire in such systems. Of particular emphasis is how temporal changes in magnetospheric source plasma and fields affect the development of auroral acceleration potentials at lower altitudes.

  20. Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.

    PubMed

    Oliver, Tim; Schmidt, Bertil; Nathan, Darran; Clemens, Ralf; Maskell, Douglas

    2005-08-15

    Aligning hundreds of sequences using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. We present a new approach to compute multiple sequence alignments in far shorter time using reconfigurable hardware. This results in an implementation of ClustalW with significant runtime savings on a standard off-the-shelf FPGA.

  1. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis

    PubMed Central

    Xu, Yinghua; Liu, Bin; Gröndahl-Yli-Hannuksila, Kirsi; Tan, Yajun; Feng, Lu; Kallonen, Teemu; Wang, Lichan; Peng, Ding; He, Qiushui; Wang, Lei; Zhang, Shumin

    2015-01-01

    Herd immunity can potentially induce a change of circulating viruses. However, it remains largely unknown that how bacterial pathogens adapt to vaccination. In this study, Bordetella pertussis, the causative agent of whooping cough, was selected as an example to explore possible effect of vaccination on the bacterial pathogen. We sequenced and analysed the complete genomes of 40 B. pertussis strains from Finland and China, as well as 11 previously sequenced strains from the Netherlands, where different vaccination strategies have been used over the past 50 years. The results showed that the molecular clock moved at different rates in these countries and in distinct periods, which suggested that evolution of the B. pertussis population was closely associated with the country vaccination coverage. Comparative whole-genome analyses indicated that evolution in this human-restricted pathogen was mainly characterised by ongoing genetic shift and gene loss. Furthermore, 116 SNPs were specifically detected in currently circulating ptxP3-containing strains. The finding might explain the successful emergence of this lineage and its spread worldwide. Collectively, our results suggest that the immune pressure of vaccination is one major driving force for the evolution of B. pertussis, which facilitates further exploration of the pathogenicity of B. pertussis. PMID:26283022

  2. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis.

    PubMed

    Xu, Yinghua; Liu, Bin; Gröndahl-Yli-Hannuksila, Kirsi; Tan, Yajun; Feng, Lu; Kallonen, Teemu; Wang, Lichan; Peng, Ding; He, Qiushui; Wang, Lei; Zhang, Shumin

    2015-08-18

    Herd immunity can potentially induce a change of circulating viruses. However, it remains largely unknown that how bacterial pathogens adapt to vaccination. In this study, Bordetella pertussis, the causative agent of whooping cough, was selected as an example to explore possible effect of vaccination on the bacterial pathogen. We sequenced and analysed the complete genomes of 40 B. pertussis strains from Finland and China, as well as 11 previously sequenced strains from the Netherlands, where different vaccination strategies have been used over the past 50 years. The results showed that the molecular clock moved at different rates in these countries and in distinct periods, which suggested that evolution of the B. pertussis population was closely associated with the country vaccination coverage. Comparative whole-genome analyses indicated that evolution in this human-restricted pathogen was mainly characterised by ongoing genetic shift and gene loss. Furthermore, 116 SNPs were specifically detected in currently circulating ptxP3-containing strains. The finding might explain the successful emergence of this lineage and its spread worldwide. Collectively, our results suggest that the immune pressure of vaccination is one major driving force for the evolution of B. pertussis, which facilitates further exploration of the pathogenicity of B. pertussis.

  3. Nucleotide sequence of a cloned woodchuck hepatitis virus genome: evolutional relationship between hepadnaviruses.

    PubMed Central

    Kodama, K; Ogasawara, N; Yoshikawa, H; Murakami, S

    1985-01-01

    We have determined the complete nucleotide sequence of a cloned DNA of woodchuck hepatitis virus (WHV), the most oncogenic virus among hepadnaviruses. The genome, designated WHV2, is 3,320 base pairs long and contains four major open reading frames (ORFs) coded on the same strand of nucleotide sequence as in the human hepatitis B virus (HBV) genome. Comparison of the nucleotide sequence and amino acid sequences deduced from it among the genomes of various hepadnaviruses demonstrates that each protein shows an intrinsic property in conserving its amino acid sequence. A parameter, the ratio of the number of triplets with one-letter change but no amino acid substitution to the total number of triplets in which one-letter change occurred, was introduced to measure the intrinsic properties quantitatively. For each ORF, the parameter gave characteristic values in all combinations. Therefore, the relative evolutional distance between these hepadnaviruses can be measured by the amino acid substitution rate of any ORF. These comparisons suggest that (i) the difference between two WHV clones, WHV1 and WHV2, corresponds to that among clones of a HBV subtype, HBVadr, and (ii) WHV and ground squirrel hepatitis virus can be categorized in a way similar to the subgroups of HBV. PMID:3855246

  4. Galaxy Zoo Hubble: First results of the redshift evolution of disk fraction in the red sequence

    NASA Astrophysics Data System (ADS)

    Galloway, Melanie; Willett, Kyle; Fortson, Lucy; Scarlata, Claudia; Beck, Melanie; Masters, Karen; Melvin, Tom

    2016-01-01

    The transition of galaxies from the blue cloud to the red sequence is commonly linked to a morphological transformation from disk to elliptical structure. However, the correlation between color and morphology is not one-to-one, as evidenced by the existence of a significant population of red disks. As this stage in a galaxy's evolution is likely to be transitory, the mechanism by which red disks are formed offers insight to the processes that trigger quenching of star formation and the galaxy's position on the star-forming sequence. To study the population of disk galaxies in the red sequence as a function of cosmic time, we utilize data from the Galaxy Zoo: Hubble project, which uses crowdsourced visual classifications of images of galaxies selected from the AEGIS, COSMOS, GEMS, and GOODS surveys. We construct a large sample of over 10,000 disk galaxies spanning a wide (0 < z < 1.0) redshift range. We use this sample to examine the change in the fraction of disks in the red sequence with respect to all disks from z˜1 to the present day. Preliminary results confirm that the fraction of disks in the red sequence decreases as the Universe evolves. We discuss the quenching processes which may explain this trend, and which morphological transformations are most affected by it.

  5. Amino acid sequences of lower vertebrate parvalbumins and their evolution: parvalbumins of boa, turtle, and salamander.

    PubMed

    Maeda, N; Zhu, D X; Fitch, W M

    1984-11-01

    One major parvalbumin each was isolated from the skeletal muscle of two reptiles, a boa snake, Boa constrictor, and a map turtle, Graptemys geographica, while two parvalbumins were isolated from an amphibian, the salamander Amphiuma means. The amino acid sequences of all four parvalbumins were determined from the sequences of their tryptic peptides, which were ordered partially by homology to other parvalbumins. Phylogenetic study of these and 16 other parvalbumin sequences revealed that the turtle parvalbumin belongs to beta lineage, while the salamander sequences belong, one each, to the alpha and beta lineages defined by Goodman and Pechère (1977). Boa parvalbumin, however, while belonging to the beta lineage, clusters within the fish in all reasonably parsimonious trees. The most parsimonious trees show many parallel or back mutations in the evolution of many parvalbumin residues, although the residues responsible for Ca2+ binding are very well conserved. These most parsimonious trees show an actinopterygian rather than a crossoptyrigian origin of the tetrapods in both the alpha and beta groups. One of two electric eel parvalbumins is evolving more than 10 times faster than its paralogous partner, suggesting it may be on its way to becoming a pseudogene. It is concluded that varying rates of amino acid replacement, much homoplasy, considerable gene duplication, plus complicated lineages make the set of parvalbumin sequences unsuitable for systematic study of the origin of the tetrapods and other higher-taxa divergence, although it may be suitable within a genus or family.

  6. Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features.

    PubMed

    Dong, Songyu; Kumazawa, Yoshinori

    2005-07-01

    Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNALeu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.

  7. Quantification of hepatic blood flow using a high-resolution phase-contrast MRI sequence with compressed sensing acceleration.

    PubMed

    Dyvorne, Hadrien A; Knight-Greenfield, Ashley; Besa, Cecilia; Cooper, Nancy; Garcia-Flores, Julio; Schiano, Thomas D; Markl, Michael; Taouli, Bachir

    2015-03-01

    OBJECTIVE. The objective of our study was to evaluate the performance of a high-spatial-resolution 2D phase-contrast (PC) MRI technique accelerated with compressed sensing for portal vein (PV) and hepatic artery (HA) flow quantification in comparison with a standard PC MRI sequence. SUBJECTS AND METHODS. In this prospective study, two PC MRI sequences were compared, one with parallel imaging acceleration and low spatial resolution (generalized autocalibrating partial parallel acquisition [GRAPPA]) and one with compressed sensing acceleration and high spatial resolution (sparse). Seventy-six patients were assessed, including 37 patients with cirrhosis. Two observers evaluated PC image quality. Quantitative analyses yielded a mean velocity, flow, and vessel area for the PV and HA and an arterial fraction. The PC techniques were compared using the paired Wilcoxon test and Bland-Altman statistics. The sensitivity of the flow parameters to the severity of cirrhosis was also assessed. RESULTS. Vessel delineation was significantly improved using the PC sparse sequence (p < 0.034). For both in vitro and in vivo measurements, PC sparse yielded lower estimates for vessel area and flow, and larger differences between PC GRAPPA and PC sparse were observed in the HA. PV velocity and flow were significantly lower in patients with cirrhosis on both PC sparse (p < 0.001 and p = 0.042, respectively) and PC GRAPPA (p < 0.001 and p = 0.005, respectively). PV velocity correlated negatively with Child-Pugh class (r = -0.50, p < 0.001), whereas the arterial fraction measured with PC sparse was higher in patients with Child-Pugh class B or C disease than in those with Child-Pugh class A disease, with a trend toward significance (p = 0.055). CONCLUSION. A high-spatial-resolution highly accelerated compressed sensing technique (PC sparse) allows total hepatic blood flow measurements obtained in 1 breath-hold, provides improved delineation of the hepatic vessels compared with a standard PC

  8. Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution.

    PubMed

    Wang, Jianping; Na, Jong-Kuk; Yu, Qingyi; Gschwend, Andrea R; Han, Jennifer; Zeng, Fanchang; Aryal, Rishi; VanBuren, Robert; Murray, Jan E; Zhang, Wenli; Navajas-Pérez, Rafael; Feltus, F Alex; Lemke, Cornelia; Tong, Eric J; Chen, Cuixia; Wai, Ching Man; Singh, Ratnesh; Wang, Ming-Li; Min, Xiang Jia; Alam, Maqsudul; Charlesworth, Deborah; Moore, Paul H; Jiang, Jiming; Paterson, Andrew H; Ming, Ray

    2012-08-21

    Sex determination in papaya is controlled by a recently evolved XY chromosome pair, with two slightly different Y chromosomes controlling the development of males (Y) and hermaphrodites (Y(h)). To study the events of early sex chromosome evolution, we sequenced the hermaphrodite-specific region of the Y(h) chromosome (HSY) and its X counterpart, yielding an 8.1-megabase (Mb) HSY pseudomolecule, and a 3.5-Mb sequence for the corresponding X region. The HSY is larger than the X region, mostly due to retrotransposon insertions. The papaya HSY differs from the X region by two large-scale inversions, the first of which likely caused the recombination suppression between the X and Y(h) chromosomes, followed by numerous additional chromosomal rearrangements. Altogether, including the X and/or HSY regions, 124 transcription units were annotated, including 50 functional pairs present in both the X and HSY. Ten HSY genes had functional homologs elsewhere in the papaya autosomal regions, suggesting movement of genes onto the HSY, whereas the X region had none. Sequence divergence between 70 transcripts shared by the X and HSY revealed two evolutionary strata in the X chromosome, corresponding to the two inversions on the HSY, the older of which evolved about 7.0 million years ago. Gene content differences between the HSY and X are greatest in the older stratum, whereas the gene content and order of the collinear regions are identical. Our findings support theoretical models of early sex chromosome evolution.

  9. Sequence evolution and expression regulation of stress-responsive genes in natural populations of wild tomato.

    PubMed

    Fischer, Iris; Steige, Kim A; Stephan, Wolfgang; Mboup, Mamadou

    2013-01-01

    The wild tomato species Solanum chilense and S. peruvianum are a valuable non-model system for studying plant adaptation since they grow in diverse environments facing many abiotic constraints. Here we investigate the sequence evolution of regulatory regions of drought and cold responsive genes and their expression regulation. The coding regions of these genes were previously shown to exhibit signatures of positive selection. Expression profiles and sequence evolution of regulatory regions of members of the Asr (ABA/water stress/ripening induced) gene family and the dehydrin gene pLC30-15 were analyzed in wild tomato populations from contrasting environments. For S. chilense, we found that Asr4 and pLC30-15 appear to respond much faster to drought conditions in accessions from very dry environments than accessions from more mesic locations. Sequence analysis suggests that the promoter of Asr2 and the downstream region of pLC30-15 are under positive selection in some local populations of S. chilense. By investigating gene expression differences at the population level we provide further support of our previous conclusions that Asr2, Asr4, and pLC30-15 are promising candidates for functional studies of adaptation. Our analysis also demonstrates the power of the candidate gene approach in evolutionary biology research and highlights the importance of wild Solanum species as a genetic resource for their cultivated relatives.

  10. Recovering evolutionary trees under a more realistic model of sequence evolution.

    PubMed

    Lockhart, P J; Steel, M A; Hendy, M D; Penny, D

    1994-07-01

    We report a new transformation, the LogDet, that is consistent for sequences with differing nucleotide composition and that have arisen under simple but asymmetric stochastic models of evolution. This transformation is required because existing methods tend to group sequences on the basis of their nucleotide composition, irrespective of their evolutionary history. This effect of differing nucleotide frequencies is illustrated by using a tree-selection criterion on a simple distance measure defined solely on the basis of base composition, independent of the actual sequences. The new LogDet transformation uses determinants of the observed divergence matrices and works because multiplication of determinants (real numbers) is commutative, whereas multiplication of matrices is not,except in special symmetric cases. The use of determinants thus allows more general models of evolution with a symmetric rates of nucleotide change. The transformation is illustrated on a theoretical data set (where existing methods select the wrong tree) and with three biological data sets: chloroplasts, birds/mammals (nuclear), and honeybees ( mitochondrial ) . The LogDet transformation reinforces the logical distinction between transformations on the data and tree-selection criteria. The overall conclusions from this study are that irregular A,C,G,T compositions are an important and possible general cause of patterns that can mislead tree-reconstruction methods, even when high bootstrap values are obtained. Consequently, many published studies may need to be reexamined. PMID:19391266

  11. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock.

    PubMed

    Van de Peer, Y; Neefs, J M; De Rijk, P; De Wachter, R

    1993-08-01

    The detailed descriptions now available for the secondary structure of small-ribosomal-subunit RNA, including areas of highly variable primary structure, facilitate the alignment of nucleotide sequences. However, for optimal exploitation of the information contained in the alignment, a method must be available that takes into account the local sequence variability in the computation of evolutionary distance. A quantitative definition for the variability of an alignment position is proposed in this study. It is a parameter in an equation which expresses the probability that the alignment position contains a different nucleotide in two sequences, as a function of the distance separating these sequences, i.e., the number of substitutions per nucleotide that occurred during their divergence. This parameter can be estimated from the distance matrix resulting from the conversion of pairwise sequence dissimilarities into pairwise distances. Alignment positions can then be subdivided into a number of sets of matching variability, and the average variability of each set can be derived. Next, the conversion of dissimilarity into distance can be recalculated for each set of alignment positions separately, using a modified version of the equation that corrects for multiple substitutions and changing for each set the parameter that reflects its average variability. The distances computed for each set are finally averaged, giving a more precise distance estimation. Trees constructed by the algorithm based on variability calibration have a topology markedly different from that of trees constructed from the same alignments in the absence of calibration. This is illustrated by means of trees constructed from small-ribosomal-subunit RNA sequences of Metazoa. A reconstruction of vertebrate evolution based on calibrated alignments matches the consensus view of paleontologists, contrary to trees based on uncalibrated alignments. In trees derived from sequences covering several metazoan

  12. The Role of the Y-Chromosome in the Establishment of Murine Hybrid Dysgenesis and in the Analysis of the Nucleotide Sequence Organization, Genetic Transmission and Evolution of Repeated Sequences.

    NASA Astrophysics Data System (ADS)

    Nallaseth, Ferez Soli

    The Y-chromosome presents a unique cytogenetic framework for the evolution of nucleotide sequences. Alignment of nine Y-chromosomal fragments in their increasing Y-specific/non Y-specific (male/female) sequence divergence ratios was directly and inversely related to their interspersion on these two respective genomic fractions. Sequence analysis confirmed a direct relationship between divergence ratios and the Alu, LINE-1, Satellite and their derivative oligonucleotide contents. Thus their relocation on the Y-chromosome is followed by sequence divergence rather than the well documented concerted evolution of these non-coding progenitor repeated sequences. Five of the nine Y-chromosomal fragments are non-pseudoautosomal and transcribed into heterogeneous PolyA^+ RNA and thus can be retrotransposed. Evolutionary and computer analysis identified homologous oligonucleotide tracts in several human loci suggesting common and random mechanistic origins. Dysgenic genomes represent the accelerated evolution driving sequence divergence (McClintock, 1984). Sex reversal and sterility characterizing dysgenesis occurs in C57BL/6JY ^{rm Pos} but not in 129/SvY^{rm Pos} derivative strains. High frequency, random, multi-locus deletion products of the feral Y^{ rm Pos}-chromosome are generated in the germlines of F1(C57BL/6J X 129/SvY^{ rm Pos})(male) and C57BL/6JY ^{rm Pos}(male) but not in 129/SvY^{rm Pos}(male). Equal, 10^{-1}, 10^ {-2}, and 0 copies (relative to males) of Y^{rm Pos}-specific deletion products respectively characterize C57BL/6JY ^{rm Pos} (HC), (LC), (T) and (F) females. The testes determining loci of inactive Y^{rm Pos}-chromosomes in C57BL/6JY^{rm Pos} HC females are the preferentially deleted/rearranged Y ^{rm Pos}-sequences. Disruption of regulation of plasma testosterone and hepatic MUP-A mRNA levels, TRD of a 4.7 Kbp EcoR1 fragment suggest disruption of autosomal/X-chromosomal sequences. These data and the highly repeated progenitor (Alu, GATA, LINE-1

  13. Evolution of the cytochrome P450 superfamily: sequence alignments and pharmacogenetics.

    PubMed

    Lewis, D F; Watson, E; Lake, B G

    1998-06-01

    The evolution of the cytochrome P450 (CYP) superfamily is described, with particular reference to major events in the development of biological forms during geological time. It is noted that the currently accepted timescale for the elaboration of the P450 phylogenetic tree exhibits close parallels with the evolution of terrestrial biota. Indeed, the present human P450 complement of xenobiotic-metabolizing enzymes may have originated from coevolutionary 'warfare' between plants and animals during the Devonian period about 400 million years ago. A number of key correspondences between the evolution of P450 system and the course of biological development over time, point to a mechanistic molecular biology of evolution which is consistent with a steady increase in atmospheric oxygenation beginning over 2000 million years ago, whereas dietary changes during more recent geological time may provide one possible explanation for certain species differences in metabolism. Alignment between P450 protein sequences within the same family or subfamily, together with across-family comparisons, aid the rationalization of drug metabolism specificities for different P450 isoforms, and can assist in an understanding of genetic polymorphisms in P450-mediated oxidations at the molecular level. Moreover, the variation in P450 regulatory mechanisms and inducibilities between different mammalian species are likely to have important implications for current procedures of chemical safety evaluation, which rely on pure genetic strains of laboratory bred rodents for the testing of compounds destined for human exposure.

  14. Numerical Simulation of Stress evolution and earthquake sequence of the Tibetan Plateau

    NASA Astrophysics Data System (ADS)

    Dong, Peiyu; Hu, Caibo; Shi, Yaolin

    2015-04-01

    The India-Eurasia's collision produces N-S compression and results in large thrust fault in the southern edge of the Tibetan Plateau. Differential eastern flow of the lower crust of the plateau leads to large strike-slip faults and normal faults within the plateau. From 1904 to 2014, more than 30 earthquakes of Mw > 6.5 occurred sequentially in this distinctive tectonic environment. How did the stresses evolve during the last 110 years, how did the earthquakes interact with each other? Can this knowledge help us to forecast the future seismic hazards? In this essay, we tried to simulate the evolution of the stress field and the earthquake sequence in the Tibetan plateau within the last 110 years with a 2-D finite element model. Given an initial state of stress, the boundary condition was constrained by the present-day GPS observation, which was assumed as a constant rate during the 110 years. We calculated stress evolution year by year, and earthquake would occur if stress exceed the crustal strength. Stress changes due to each large earthquake in the sequence was calculated and contributed to the stress evolution. A key issue is the choice of initial stress state of the modeling, which is actually unknown. Usually, in the study of earthquake triggering, people assume the initial stress is zero, and only calculate the stress changes by large earthquakes - the Coulomb failure stress changes (Δ CFS). To some extent, this simplified method is a powerful tool because it can reveal which fault or which part of a fault becomes more risky or safer relatively. Nonetheless, it has not utilized all information available to us. The earthquake sequence reveals, though far from complete, some information about the stress state in the region. If the entire region is close to a self-organized critical or subcritical state, earthquake stress drop provides an estimate of lower limit of initial state. For locations no earthquakes occurred during the period, initial stress has to be

  15. Genome sequence of Perigonia lusca single nucleopolyhedrovirus: insights into the evolution of a nucleotide metabolism enzyme in the family Baculoviridae

    PubMed Central

    Ardisson-Araújo, Daniel M. P.; Lima, Rayane Nunes; Melo, Fernando L.; Clem, Rollie J.; Huang, Ning; Báo, Sônia Nair; Sosa-Gómez, Daniel R.; Ribeiro, Bergmann M.

    2016-01-01

    The genome of a novel group II alphabaculovirus, Perigonia lusca single nucleopolyhedrovirus (PeluSNPV), was sequenced and shown to contain 132,831 bp with 145 putative ORFs (open reading frames) of at least 50 amino acids. An interesting feature of this novel genome was the presence of a putative nucleotide metabolism enzyme-encoding gene (pelu112). The pelu112 gene was predicted to encode a fusion of thymidylate kinase (tmk) and dUTP diphosphatase (dut). Phylogenetic analysis indicated that baculoviruses have independently acquired tmk and dut several times during their evolution. Two homologs of the tmk-dut fusion gene were separately introduced into the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) genome, which lacks tmk and dut. The recombinant baculoviruses produced viral DNA, virus progeny, and some viral proteins earlier during in vitro infection and the yields of viral occlusion bodies were increased 2.5-fold when compared to the parental virus. Interestingly, both enzymes appear to retain their active sites, based on separate modeling using previously solved crystal structures. We suggest that the retention of these tmk-dut fusion genes by certain baculoviruses could be related to accelerating virus replication and to protecting the virus genome from deleterious mutation. PMID:27273152

  16. SW#db: GPU-Accelerated Exact Sequence Similarity Database Search

    PubMed Central

    Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

    2015-01-01

    In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result–the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4–5 times faster than SSEARCH, 6–25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases PMID:26719890

  17. SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

    PubMed

    Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

    2015-01-01

    In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases. PMID:26719890

  18. Cytochrome B sequences suggest convergent evolution of the Asian takin and Arctic muskox.

    PubMed

    Groves, P; Shields, G F

    1997-12-01

    Relationships of the takin (Budorcas taxicolor) and muskox (Ovibos moschatus) have been speculated upon for many years. Morphological and behavioral similarities between these species have led to suggestions that they are closely related. To test the hypothesis that characteristics shared by the takin and muskox stem from a recent common ancestor, we compared sequences of their mitochondrial cytochrome b genes with those of three other species of Caprinae. We present data that may support rejection of the hypothesis of recent common ancestry and suggest that similarities in behavior and morphology in these two species might be attributed to convergent evolution rather than shared phylogeny.

  19. Cytochrome B sequences suggest convergent evolution of the Asian takin and Arctic muskox.

    PubMed

    Groves, P; Shields, G F

    1997-12-01

    Relationships of the takin (Budorcas taxicolor) and muskox (Ovibos moschatus) have been speculated upon for many years. Morphological and behavioral similarities between these species have led to suggestions that they are closely related. To test the hypothesis that characteristics shared by the takin and muskox stem from a recent common ancestor, we compared sequences of their mitochondrial cytochrome b genes with those of three other species of Caprinae. We present data that may support rejection of the hypothesis of recent common ancestry and suggest that similarities in behavior and morphology in these two species might be attributed to convergent evolution rather than shared phylogeny. PMID:9417894

  20. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.

    PubMed

    Green, Robert C; Goddard, Katrina A B; Jarvik, Gail P; Amendola, Laura M; Appelbaum, Paul S; Berg, Jonathan S; Bernhardt, Barbara A; Biesecker, Leslie G; Biswas, Sawona; Blout, Carrie L; Bowling, Kevin M; Brothers, Kyle B; Burke, Wylie; Caga-Anan, Charlisse F; Chinnaiyan, Arul M; Chung, Wendy K; Clayton, Ellen W; Cooper, Gregory M; East, Kelly; Evans, James P; Fullerton, Stephanie M; Garraway, Levi A; Garrett, Jeremy R; Gray, Stacy W; Henderson, Gail E; Hindorff, Lucia A; Holm, Ingrid A; Lewis, Michelle Huckaby; Hutter, Carolyn M; Janne, Pasi A; Joffe, Steven; Kaufman, David; Knoppers, Bartha M; Koenig, Barbara A; Krantz, Ian D; Manolio, Teri A; McCullough, Laurence; McEwen, Jean; McGuire, Amy; Muzny, Donna; Myers, Richard M; Nickerson, Deborah A; Ou, Jeffrey; Parsons, Donald W; Petersen, Gloria M; Plon, Sharon E; Rehm, Heidi L; Roberts, J Scott; Robinson, Dan; Salama, Joseph S; Scollon, Sarah; Sharp, Richard R; Shirts, Brian; Spinner, Nancy B; Tabor, Holly K; Tarczy-Hornoch, Peter; Veenstra, David L; Wagle, Nikhil; Weck, Karen; Wilfond, Benjamin S; Wilhelmsen, Kirk; Wolf, Susan M; Wynn, Julia; Yu, Joon-Ho

    2016-06-01

    Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.

  1. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.

    PubMed

    Green, Robert C; Goddard, Katrina A B; Jarvik, Gail P; Amendola, Laura M; Appelbaum, Paul S; Berg, Jonathan S; Bernhardt, Barbara A; Biesecker, Leslie G; Biswas, Sawona; Blout, Carrie L; Bowling, Kevin M; Brothers, Kyle B; Burke, Wylie; Caga-Anan, Charlisse F; Chinnaiyan, Arul M; Chung, Wendy K; Clayton, Ellen W; Cooper, Gregory M; East, Kelly; Evans, James P; Fullerton, Stephanie M; Garraway, Levi A; Garrett, Jeremy R; Gray, Stacy W; Henderson, Gail E; Hindorff, Lucia A; Holm, Ingrid A; Lewis, Michelle Huckaby; Hutter, Carolyn M; Janne, Pasi A; Joffe, Steven; Kaufman, David; Knoppers, Bartha M; Koenig, Barbara A; Krantz, Ian D; Manolio, Teri A; McCullough, Laurence; McEwen, Jean; McGuire, Amy; Muzny, Donna; Myers, Richard M; Nickerson, Deborah A; Ou, Jeffrey; Parsons, Donald W; Petersen, Gloria M; Plon, Sharon E; Rehm, Heidi L; Roberts, J Scott; Robinson, Dan; Salama, Joseph S; Scollon, Sarah; Sharp, Richard R; Shirts, Brian; Spinner, Nancy B; Tabor, Holly K; Tarczy-Hornoch, Peter; Veenstra, David L; Wagle, Nikhil; Weck, Karen; Wilfond, Benjamin S; Wilhelmsen, Kirk; Wolf, Susan M; Wynn, Julia; Yu, Joon-Ho

    2016-06-01

    Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine. PMID:27181682

  2. Parameters of the proteome evolution from the distribution of sequence identities of paralogous proteins

    NASA Astrophysics Data System (ADS)

    Yan, Koon-Kiu; Axelsen, Jacob; Maslov, Sergei

    2006-03-01

    The evolution of the full repertoire of proteins encoded in a given genome is driven by gene duplications, deletions and modifications of amino-acid sequences of already existing proteins. The information about relative rates and other intrinsic parameters of these three basic processes is contained in the distribution of sequence identities of pairs of paralogous proteins. We introduced a simple mathematical framework that allows one to extract some of this hidden information. It was then applied to the proteome-wide set of paralogous proteins in H. pylori, E. coli, S. cerevisiae, C. elegans, D. melanogaster and H. sapiens. We estimated the stationary per-gene deletion and duplication rates, the distribution of amino-acid substitution rate of these organisms. The validity of our mathematical framework was further confirmed by numerical simulations of a simple evolutionary model of a fixed-size proteome.

  3. Dynamic evolution of telomeric sequences in the green algal order Chlamydomonadales.

    PubMed

    Fulnečková, Jana; Hasíková, Tereza; Fajkus, Jiří; Lukešová, Alena; Eliáš, Marek; Sýkorová, Eva

    2012-01-01

    Telomeres, which form the protective ends of eukaryotic chromosomes, are a ubiquitous and conserved structure of eukaryotic genomes but the basic structural unit of most telomeres, a repeated minisatellite motif with the general consensus sequence T(n)A(m)G(o), may vary between eukaryotic groups. Previous studies on several species of green algae revealed that this group exhibits at least two types of telomeric sequences, a presumably ancestral type shared with land plants (Arabidopsis type, TTTAGGG) and conserved in, for example, Ostreococcus and Chlorella species, and a novel type (Chlamydomonas type, TTTTAGGG) identified in Chlamydomonas reinhardtii. We have employed several methodical approaches to survey the diversity of telomeric sequences in a phylogenetically wide array of green algal species, focusing on the order Chlamydomonadales. Our results support the view that the Arabidopsis-type telomeric sequence is ancestral for green algae and has been conserved in most lineages, including Mamiellophyceae, Chlorodendrophyceae, Trebouxiophyceae, Sphaeropleales, and most Chlamydomonadales. However, within the Chlamydomonadales, at least two independent evolutionary changes to the Chlamydomonas type occurred, specifically in a subgroup of the Reinhardtinia clade (including C. reinhardtii and Volvox carteri) and in the Chloromonadinia clade. Furthermore, a complex structure of telomeric repeats, including a mix of the ancestral Arabidopsis-type motifs and derived motifs identical to the human-type telomeric repeats (TTAGGG), was found in the chlamydomonadalean clades Dunaliellinia and Stephanosphaeria. Our results indicate that telomere evolution in green algae, particularly in the order Chlamydomonadales, is far more dynamic and complex than thought before. General implications of our findings for the mode of telomere evolution are discussed. PMID:22247428

  4. Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution.

    PubMed

    Cai, Hui; Thompson, Rebecca; Budinich, Mateo F; Broadbent, Jeff R; Steele, James L

    2009-01-01

    Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei. PMID:20333194

  5. The quick and the fast: the evolution of acceleration capacity in Anolis lizards.

    PubMed

    Vanhooydonck, Bieke; Herrel, Anthony; Van Damme, Raoul; Irschick, Duncan J

    2006-10-01

    Although of prime ecological relevance, acceleration capacity is a poorly understood locomotor performance trait in terrestrial vertebrates. No empirical data exist on which design characteristics determine acceleration capacity among species and whether these design traits influence other aspects of locomotor performance. In this study we explore how acceleration capacity and sprint speed have evolved in Anolis lizards. We investigate whether the same or different morphological traits (i.e., limb dimensions and muscle mass) correlate with both locomotor traits. Within our sample of Anolis lizards, relative sprint speed and acceleration capacity coevolved. However, whereas the variation in relative acceleration capacity is primarily explained by the variation in relative knee extensor muscle mass, the variation in relative sprint speed is correlated to the variation in relative femur, tibia, and metatarsus length as well as knee extensor muscle mass. The fact that the design features required to excel in either performance trait partly overlap might explain the positive correlation between the variation in relative sprint speed and acceleration capacity. Furthermore, our data show how similar levels of sprint performance can be achieved through different morphological traits (limb segment lengths and muscle mass) suggesting that redundant mapping has potentially played a role in mitigating trade-offs.

  6. Spatiotemporal evolution of electron characteristics in the electron diffusion region of magnetic reconnection: Implications for acceleration and heating

    NASA Astrophysics Data System (ADS)

    Shuster, J. R.; Chen, L.-J.; Hesse, M.; Argall, M. R.; Daughton, W.; Torbert, R. B.; Bessho, N.

    2015-04-01

    Based on particle-in-cell simulations of collisionless magnetic reconnection, the spatiotemporal evolution of electron velocity distributions in the electron diffusion region (EDR) is reported to illustrate how electrons are accelerated and heated. Approximately when the reconnection rate maximizes, electron distributions in the vicinity of the X line exhibit triangular structures with discrete striations and a temperature (Te) twice that of the inflow region. Te increases as the meandering EDR populations mix with inflowing electrons. As the distance from the X line increases within the electron outflow jet, the discrete populations swirl into arcs and gyrotropize by the end of the jet with Te about 3 times that of the X line. Two dominant processes increase Te and produce the spatially and temporally evolving EDR distributions: (1) electric field acceleration preferential to electrons which meander in the EDR for longer times and (2) cyclotron turning by the magnetic field normal to the reconnection layer.

  7. Sequence divergence and chromosomal rearrangements during the evolution of human pseudoautosomal genes and their mouse homologs

    SciTech Connect

    Ellison, J.; Li, X.; Francke, U.

    1994-09-01

    The pseudoautosomal region (PAR) is an area of sequence identity between the X and Y chromosomes and is important for mediating X-Y pairing during male meiosis. Of the seven genes assigned to the human PAR, none of the mouse homologs have been isolated by a cross-hybridization strategy. Two of these homologs, Csfgmra and II3ra, have been isolated using a functional assay for the gene products. These genes are quite different in sequence from their human homologs, showing only 60-70% sequence similarity. The Csfgmra gene has been found to further differ from its human homolog in being isolated not on the sex chromosomes, but on a mouse autosome (chromosome 19). Using a mouse-hamster somatic cell hybrid mapping panel, we have mapped the II3ra gene to yet another mouse autosome, chromosome 14. Attempts to clone the mouse homolog of the ANT3 locus resulted in the isolation of two related genes, Ant1 and Ant2, but failed to yield the Ant3 gene. Southern blot analysis of the ANT/Ant genes showed the Ant1 and Ant2 sequences to be well-conserved among all of a dozen mammals tested. In contrast, the ANT3 gene only showed hybridization to non-rodent mammals, suggesting it is either greatly divergent or has been deleted in the rodent lineage. Similar experiments with other human pseudoautosomal probes likewise showed a lack of hybridization to rodent sequences. The results show a definite trend of extensive divergence of pseudoautosomal sequences in addition to chromosomal rearrangements involving X;autosome translocations and perhaps gene deletions. Such observations have interesting implications regarding the evolution of this important region of the sex chromosomes.

  8. [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].

    PubMed

    Korkosh, V S; Zhorov, B S; Tikhonov, D B

    2016-01-01

    An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

  9. Protecting and accelerating adiabatic passage with time-delayed pulse sequences.

    PubMed

    Sampedro, Pablo; Chang, Bo Y; Sola, Ignacio R

    2016-05-21

    Using numerical simulations of two-photon electronic absorption with femtosecond pulses in Na2 we show that: (i) it is possible to avoid the characteristic saturation or dumped Rabi oscillations in the yield of absorption by time-delaying the laser pulses; (ii) it is possible to accelerate the onset of adiabatic passage by using the vibrational coherence starting in a wave packet; and (iii) it is possible to prepare the initial wave packet in order to achieve full state-selective transitions with broadband pulses. The findings can be used, for instance, to achieve ultrafast adiabatic passage by light-induced potentials and understand its intrinsic robustness. PMID:27125342

  10. Protecting and accelerating adiabatic passage with time-delayed pulse sequences.

    PubMed

    Sampedro, Pablo; Chang, Bo Y; Sola, Ignacio R

    2016-05-21

    Using numerical simulations of two-photon electronic absorption with femtosecond pulses in Na2 we show that: (i) it is possible to avoid the characteristic saturation or dumped Rabi oscillations in the yield of absorption by time-delaying the laser pulses; (ii) it is possible to accelerate the onset of adiabatic passage by using the vibrational coherence starting in a wave packet; and (iii) it is possible to prepare the initial wave packet in order to achieve full state-selective transitions with broadband pulses. The findings can be used, for instance, to achieve ultrafast adiabatic passage by light-induced potentials and understand its intrinsic robustness.

  11. Efficient numerical modelling of the emittance evolution of beams with finite energy spread in plasma wakefield accelerators

    NASA Astrophysics Data System (ADS)

    Mehrling, T. J.; Robson, R. E.; Erbe, J.-H.; Osterhoff, J.

    2016-09-01

    This paper introduces a semi-analytic numerical approach (SANA) for the rapid computation of the transverse emittance of beams with finite energy spread in plasma wakefield accelerators in the blowout regime. The SANA method is used to model the beam emittance evolution when injected into and extracted from realistic plasma profiles. Results are compared to particle-in-cell simulations, establishing the accuracy and efficiency of the procedure. In addition, it is demonstrated that the tapering of vacuum-to-plasma and plasma-to-vacuum transitions is a viable method for the mitigation of emittance growth of beams during their injection and extraction from and into plasma cells.

  12. Complete Chloroplast Genome Sequence of Aquilaria sinensis (Lour.) Gilg and Evolution Analysis within the Malvales Order

    PubMed Central

    Wang, Ying; Zhan, Di-Feng; Jia, Xian; Mei, Wen-Li; Dai, Hao-Fu; Chen, Xiong-Ting; Peng, Shi-Qing

    2016-01-01

    Aquilaria sinensis (Lour.) Gilg is an important medicinal woody plant producing agarwood, which is widely used in traditional Chinese medicine. High-throughput sequencing of chloroplast (cp) genomes enhanced the understanding about evolutionary relationships within plant families. In this study, we determined the complete cp genome sequences for A. sinensis. The size of the A. sinensis cp genome was 159,565 bp. This genome included a large single-copy region of 87,482 bp, a small single-copy region of 19,857 bp, and a pair of inverted repeats (IRa and IRb) of 26,113 bp each. The GC content of the genome was 37.11%. The A. sinensis cp genome encoded 113 functional genes, including 82 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. A total of 45 polymorphic simple-sequence repeat loci and 60 pairs of large repeats were identified. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited high A/T content. Moreover, 33 pairs of large repeat sequences were located in the protein-coding genes, whereas 27 pairs were located in the intergenic regions. Aquilaria sinensis cp genome bias ended with A/T on the basis of codon usage. The distribution of codon usage in A. sinensis cp genome was most similar to that in the Gonystylus bancanus cp genome. Comparative results of 82 protein-coding genes from 29 species of cp genomes demonstrated that A. sinensis was a sister species to G. bancanus within the Malvales order. Aquilaria sinensis cp genome presented the highest sequence similarity of >90% with the G. bancanus cp genome by using CGView Comparison Tool. This finding strongly supports the placement of A. sinensis as a sister to G. bancanus within the Malvales order. The complete A. sinensis cp genome information will be highly beneficial for further studies on this traditional medicinal

  13. Improved measurement of brain deformation during mild head acceleration using a novel tagged MRI sequence.

    PubMed

    Knutsen, Andrew K; Magrath, Elizabeth; McEntee, Julie E; Xing, Fangxu; Prince, Jerry L; Bayly, Philip V; Butman, John A; Pham, Dzung L

    2014-11-01

    In vivo measurements of human brain deformation during mild acceleration are needed to help validate computational models of traumatic brain injury and to understand the factors that govern the mechanical response of the brain. Tagged magnetic resonance imaging is a powerful, noninvasive technique to track tissue motion in vivo which has been used to quantify brain deformation in live human subjects. However, these prior studies required from 72 to 144 head rotations to generate deformation data for a single image slice, precluding its use to investigate the entire brain in a single subject. Here, a novel method is introduced that significantly reduces temporal variability in the acquisition and improves the accuracy of displacement estimates. Optimization of the acquisition parameters in a gelatin phantom and three human subjects leads to a reduction in the number of rotations from 72 to 144 to as few as 8 for a single image slice. The ability to estimate accurate, well-resolved, fields of displacement and strain in far fewer repetitions will enable comprehensive studies of acceleration-induced deformation throughout the human brain in vivo.

  14. Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution.

    PubMed

    Thacker, Robert W; Hill, April L; Hill, Malcolm S; Redmond, Niamh E; Collins, Allen G; Morrow, Christine C; Spicer, Lori; Carmack, Cheryl A; Zappe, Megan E; Pohlmann, Deborah; Hall, Chelsea; Diaz, Maria C; Bangalore, Purushotham V

    2013-09-01

    The highly collaborative research sponsored by the NSF-funded Assembling the Porifera Tree of Life (PorToL) project is providing insights into some of the most difficult questions in metazoan systematics. Our understanding of phylogenetic relationships within the phylum Porifera has changed considerably with increased taxon sampling and data from additional molecular markers. PorToL researchers have falsified earlier phylogenetic hypotheses, discovered novel phylogenetic alliances, found phylogenetic homes for enigmatic taxa, and provided a more precise understanding of the evolution of skeletal features, secondary metabolites, body organization, and symbioses. Some of these exciting new discoveries are shared in the papers that form this issue of Integrative and Comparative Biology. Our analyses of over 300 nearly complete 28S ribosomal subunit gene sequences provide specific case studies that illustrate how our dataset confirms new hypotheses of sponge evolution. We recovered monophyletic clades for all 4 classes of sponges, as well as the 4 major clades of Demospongiae (Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha), but our phylogeny differs in several aspects from traditional classifications. In most major clades of sponges, families within orders appear to be paraphyletic. Although additional sampling of genes and taxa are needed to establish whether this pattern results from a lack of phylogenetic resolution or from a paraphyletic classification system, many of our results are congruent with those obtained from 18S ribosomal subunit gene sequences and complete mitochondrial genomes. These data provide further support for a revision of the traditional classification of sponges. PMID:23748742

  15. Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution.

    PubMed Central

    Saier, M H

    1994-01-01

    Three-dimensional structures have been elucidated for very few integral membrane proteins. Computer methods can be used as guides for estimation of solute transport protein structure, function, biogenesis, and evolution. In this paper the application of currently available computer programs to over a dozen distinct families of transport proteins is reviewed. The reliability of sequence-based topological and localization analyses and the importance of sequence and residue conservation to structure and function are evaluated. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific transport protein families is also evaluated. Channel proteins are proposed to be functionally related to carriers. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is shown that several transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes. The possible significance of this apparent topological convergence is discussed. PMID:8177172

  16. Nearly Complete 28S rRNA Gene Sequences Confirm New Hypotheses of Sponge Evolution

    PubMed Central

    Thacker, Robert W.; Hill, April L.; Hill, Malcolm S.; Redmond, Niamh E.; Collins, Allen G.; Morrow, Christine C.; Spicer, Lori; Carmack, Cheryl A.; Zappe, Megan E.; Pohlmann, Deborah; Hall, Chelsea; Diaz, Maria C.; Bangalore, Purushotham V.

    2013-01-01

    The highly collaborative research sponsored by the NSF-funded Assembling the Porifera Tree of Life (PorToL) project is providing insights into some of the most difficult questions in metazoan systematics. Our understanding of phylogenetic relationships within the phylum Porifera has changed considerably with increased taxon sampling and data from additional molecular markers. PorToL researchers have falsified earlier phylogenetic hypotheses, discovered novel phylogenetic alliances, found phylogenetic homes for enigmatic taxa, and provided a more precise understanding of the evolution of skeletal features, secondary metabolites, body organization, and symbioses. Some of these exciting new discoveries are shared in the papers that form this issue of Integrative and Comparative Biology. Our analyses of over 300 nearly complete 28S ribosomal subunit gene sequences provide specific case studies that illustrate how our dataset confirms new hypotheses of sponge evolution. We recovered monophyletic clades for all 4 classes of sponges, as well as the 4 major clades of Demospongiae (Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha), but our phylogeny differs in several aspects from traditional classifications. In most major clades of sponges, families within orders appear to be paraphyletic. Although additional sampling of genes and taxa are needed to establish whether this pattern results from a lack of phylogenetic resolution or from a paraphyletic classification system, many of our results are congruent with those obtained from 18S ribosomal subunit gene sequences and complete mitochondrial genomes. These data provide further support for a revision of the traditional classification of sponges. PMID:23748742

  17. Ectodomain Architecture Affects Sequence and Functional Evolution of Vertebrate Toll-like Receptors.

    PubMed

    Wang, Jinlan; Zhang, Zheng; Liu, Jing; Zhao, Jing; Yin, Deling

    2016-01-01

    Toll-like receptors (TLRs) are crucial components of innate immunity that specifically recognize diverse pathogen-associated molecular patterns from pathogens. The continuous hydrogen-bond network (asparagine ladder) formed among the asparagine residues on the concave surfaces of neighboring leucine-rich repeat modules assists in stabilizing the overall shape of TLR ectodomains responsible for ligand recognition. Analysis of 28 types of vertebrate TLRs showed that their ectodomains possessed three types of architectures: a single-domain architecture with an intact asparagine ladder, a three-domain architecture with the ladder interrupted in the middle, and a trans-three-domain architecture with the ladder broken in both termini. Based on a phylogenetic analysis, the three vertebrate TLR architectures arose during early evolution. The 1428 vertebrate TLRs can be divided into eight families based on sequence and structural differences. TLRs ligand specificities are affected by their ectodomain architectures. Three-domain TLRs bind hydrophobic ligands, whereas single-domain and trans-three-domain TLRs mainly recognize hydrophilic ligands. Analysis of 39 vertebrate genomes suggested that the number of single-domain TLR genes in terrestrial vertebrate genomes decreased by half compared to aquatic vertebrate genomes. Single-domain TLR genes underwent stronger purifying selective pressures than three-domain TLR genes in mammals. Overall, ectodomain architecture influences the sequence and functional evolution of vertebrate TLRs. PMID:27216145

  18. DNA sequence-dependent morphological evolution of silver nanoparticles and their optical and hybridization properties.

    PubMed

    Wu, Jiangjiexing; Tan, Li Huey; Hwang, Kevin; Xing, Hang; Wu, Peiwen; Li, Wei; Lu, Yi

    2014-10-29

    A systematic investigation of the effects of different DNA sequences on the morphologies of silver nanoparticles (AgNPs) grown from Ag nanocube seeds is reported. The presence of 10-mer oligo-A, -T, and -C directed AgNPs growth from cubic seeds into edge-truncated octahedra of different truncation extents and truncated tetrahedral AgNPs, while AgNPs in the presence of oligo-G remained cubic. The shape and morphological evolution of the nanoparticle growth for each system is investigated using SEM and TEM and correlated with UV-vis absorption kinetic studies. In addition, the roles of oligo-C and oligo-G secondary structures in modulating the morphologies of AgNPs are elucidated, and the morphological evolution for each condition of AgNPs growth is proposed. The shapes were found to be highly dependent on the binding affinity of each of the bases and the DNA secondary structures, favoring the stabilization of the Ag{111} facet. The AgNPs synthesized through this method have morphologies and optical properties that can be varied by using different DNA sequences, while the DNA molecules on these AgNPs are also stable against glutathione. The AgNP functionalization can be realized in a one-step synthesis while retaining the biorecognition ability of the DNA, which allows for programmable assembly. PMID:25243485

  19. Ectodomain Architecture Affects Sequence and Functional Evolution of Vertebrate Toll-like Receptors

    PubMed Central

    Wang, Jinlan; Zhang, Zheng; Liu, Jing; Zhao, Jing; Yin, Deling

    2016-01-01

    Toll-like receptors (TLRs) are crucial components of innate immunity that specifically recognize diverse pathogen-associated molecular patterns from pathogens. The continuous hydrogen-bond network (asparagine ladder) formed among the asparagine residues on the concave surfaces of neighboring leucine-rich repeat modules assists in stabilizing the overall shape of TLR ectodomains responsible for ligand recognition. Analysis of 28 types of vertebrate TLRs showed that their ectodomains possessed three types of architectures: a single-domain architecture with an intact asparagine ladder, a three-domain architecture with the ladder interrupted in the middle, and a trans-three-domain architecture with the ladder broken in both termini. Based on a phylogenetic analysis, the three vertebrate TLR architectures arose during early evolution. The 1428 vertebrate TLRs can be divided into eight families based on sequence and structural differences. TLRs ligand specificities are affected by their ectodomain architectures. Three-domain TLRs bind hydrophobic ligands, whereas single-domain and trans-three-domain TLRs mainly recognize hydrophilic ligands. Analysis of 39 vertebrate genomes suggested that the number of single-domain TLR genes in terrestrial vertebrate genomes decreased by half compared to aquatic vertebrate genomes. Single-domain TLR genes underwent stronger purifying selective pressures than three-domain TLR genes in mammals. Overall, ectodomain architecture influences the sequence and functional evolution of vertebrate TLRs. PMID:27216145

  20. A LARGE STELLAR EVOLUTION DATABASE FOR POPULATION SYNTHESIS STUDIES. VI. WHITE DWARF COOLING SEQUENCES

    SciTech Connect

    Salaris, M.; Cassisi, S.; Pietrinferni, A.; Kowalski, P. M.; Isern, J. E-mail: cassisi@oa-teramo.inaf.i

    2010-06-20

    We present a new set of cooling models and isochrones for both H- and He-atmosphere white dwarfs (WDs), incorporating accurate boundary conditions from detailed model atmosphere calculations, and carbon-oxygen chemical abundance profiles based on updated stellar evolution calculations from the BaSTI stellar evolution archive-a theoretical data center for the Virtual Observatory. We discuss and quantify the uncertainties in the cooling times predicted by the models, arising from the treatment of mixing during the central H- and He-burning phases, the number of thermal pulses experienced by the progenitors, progenitor metallicity, and the {sup 12}C({alpha}, {gamma}){sup 16}O reaction rate. The largest sources of uncertainty turn out to be related to the treatment of convection during the last stages of the progenitor central He-burning phase and the {sup 12}C({alpha}, {gamma}){sup 16}O reaction rate. We compare our new models to previous calculations performed with the same stellar evolution code, and discuss their application to the estimate of the age of the solar neighborhood and the interpretation of the observed number ratios between H- and He-atmosphere WDs. The new WD sequences and an extensive set of WD isochrones that cover a large range of ages and progenitor metallicities are made publicly available at the official BaSTI Web site.

  1. Mass loss from pre-main-sequence accretion disks. I - The accelerating wind of FU Orionis

    NASA Technical Reports Server (NTRS)

    Calvet, Nuria; Hartmann, Lee; Kenyon, Scott J.

    1993-01-01

    We present evidence that the wind of the pre-main-sequence object FU Orionis arises from the surface of the luminous accretion disk. A disk wind model calculated assuming radiative equilibrium explains the differential behavior of the observed asymmetric absorption-line profiles. The model predicts that strong lines should be asymmetric and blueshifted, while weak lines should be symmetric and double-peaked due to disk rotation, in agreement with observations. We propose that many blueshifted 'shell' absorption features are not produced in a true shell of material, but rather form in a differentially expanding wind that is rapidly rotating. The inference of rapid rotation supports the proposal that pre-main-sequence disk winds are rotationally driven.

  2. Rapid Evolution of the Sequences and Gene Repertoires of Secreted Proteins in Bacteria

    PubMed Central

    Rocha, Eduardo P. C.

    2012-01-01

    Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation. PMID:23189144

  3. Comparative molecular phylogeny and evolution of sex chromosome DNA sequences in the family Canidae (Mammalia: Carnivora).

    PubMed

    Tsubouchi, Ayako; Fukui, Daisuke; Ueda, Miya; Tada, Kazumi; Toyoshima, Shouji; Takami, Kazutoshi; Tsujimoto, Tsunenori; Uraguchi, Kohji; Raichev, Evgeniy; Kaneko, Yayoi; Tsunoda, Hiroshi; Masuda, Ryuichi

    2012-03-01

    To investigate the molecular phylogeny and evolution of the family Canidae, nucleotide sequences of the zinc-finger-protein gene on the Y chromosome (ZFY, 924-1146 bp) and its homologous gene on the X chromosome (ZFX, 834-839 bp) for twelve canid species were determined. The phylogenetic relationships among species reconstructed by the paternal ZFY sequences closely agreed with those by mtDNA and autosomal DNA trees in previous reports, and strongly supported the phylogenetic affinity between the wolf-like canids clade and the South American canids clade. However, the branching order of some species differed between phylogenies of ZFY and ZFX genes: Cuon alpinus and Canis mesomelas were included in the wolf-like canid clades in the ZFY tree, whereas both species were clustered in a group of Chrysocyon brachyurus and Speothos venaticus in the ZFX tree. The topology difference between ZFY and ZFX trees may have resulted from the two-times higher substitution rate of the former than the latter, which was clarified in the present study. In addition, two types of transposable element sequence (SINE-I and SINE-II) were found to occur in the ZFY final intron of the twelve canid species examined. Because the SINE-I sequences were shared by all the species, they may have been inserted into the ZFY of the common ancestor before species radiation in Canidae. By contract, SINE-II found in only Canis aureus could have been inserted into ZFY independently after the speciation. The molecular diversity of SINE sequences of Canidae reflects evolutionary history of the species radiation. PMID:22379982

  4. BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

    PubMed Central

    Lee, Lap-Kei; Cheung, Jeanno; Liu, Chi-Man

    2014-01-01

    This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 h to process 50-fold whole genome sequencing (∼750 million 100 bp paired-end reads), or just 25 min for 210-fold whole exome sequencing. BALSA’s speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses. BALSA is available at: http://sourceforge.net/p/balsa. PMID:24949238

  5. Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates

    PubMed Central

    Figuet, Emeric; Ballenghien, Marion; Romiguier, Jonathan; Galtier, Nicolas

    2015-01-01

    Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins. PMID:25527834

  6. Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates.

    PubMed

    Figuet, Emeric; Ballenghien, Marion; Romiguier, Jonathan; Galtier, Nicolas

    2014-12-19

    Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins.

  7. Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria▿ †

    PubMed Central

    Slater, Steven C.; Goldman, Barry S.; Goodner, Brad; Setubal, João C.; Farrand, Stephen K.; Nester, Eugene W.; Burr, Thomas J.; Banta, Lois; Dickerman, Allan W.; Paulsen, Ian; Otten, Leon; Suen, Garret; Welch, Roy; Almeida, Nalvo F.; Arnold, Frank; Burton, Oliver T.; Du, Zijin; Ewing, Adam; Godsy, Eric; Heisel, Sara; Houmiel, Kathryn L.; Jhaveri, Jinal; Lu, Jing; Miller, Nancy M.; Norton, Stacie; Chen, Qiang; Phoolcharoen, Waranyoo; Ohlin, Victoria; Ondrusek, Dan; Pride, Nicole; Stricklin, Shawn L.; Sun, Jian; Wheeler, Cathy; Wilson, Lindsey; Zhu, Huijun; Wood, Derek W.

    2009-01-01

    The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria. PMID:19251847

  8. A population genetic study of the evolution of SINEs. II. Sequence evolution under the master copy model

    SciTech Connect

    Tachida, Hidenori

    1996-06-01

    A transient population genetic model of SINE (short interspersed repetitive element) evolution is presented, assuming the master copy model is theoretically investigated. Means and variances of consensus frequency of nucleotides, nucleotide homozygosity, and the number of shared differences that are considered to have been caused by mutations occurring in the master copy lineages are computed. All quantities investigated are shown to be monotone functions of the duration of the expansion period. Thus, they can be used to estimate the expansion period although their sampling variances are generally large. Using the theoretical results, the Sb subfamily of human Alu sequences is analyzed. First, the expansion period is estimated from the observed mean and variance of homozygosity. The expansion period is shown to be short compared to the time since the end of the expansion of the subfamily. However, the observed number of the shared differences is more than twice that expected under the master copy model with the estimated expansion period. Alternative models to explain this observation are discussed, including one with multiple master copy loci. 38 refs., 5 figs., 4 tabs.

  9. Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

    PubMed Central

    Tennessen, Jacob A.; Bigham, Abigail W.; O'Connor, Timothy D.; Fu, Wenqing; Kenny, Eimear E.; Gravel, Simon; McGee, Sean; Do, Ron; Liu, Xiaoming; Jun, Goo; Kang, Hyun Min; Jordan, Daniel; Leal, Suzanne M.; Gabriel, Stacey; Rieder, Mark J.; Abecasis, Goncalo; Altshuler, David; Nickerson, Deborah A.; Boerwinkle, Eric; Sunyaev, Shamil; Bustamante, Carlos D.; Bamshad, Michael J.; Akey, Joshua M.

    2013-01-01

    As a first step toward understanding how rare variants contribute to risk for complex diseases, we sequenced 15,585 human protein-coding genes to an average median depth of 111× in 2440 individuals of European (n = 1351) and African (n = 1088) ancestry. We identified over 500,000 single-nucleotide variants (SNVs), the majority of which were rare (86% with a minor allele frequency less than 0.5%), previously unknown (82%), and population-specific (82%). On average, 2.3% of the 13,595 SNVs each person carried were predicted to affect protein function of ∼313 genes per genome, and ∼95.7% of SNVs predicted to be functionally important were rare. This excess of rare functional variants is due to the combined effects of explosive, recent accelerated population growth and weak purifying selection. Furthermore, we show that large sample sizes will be required to associate rare variants with complex traits. PMID:22604720

  10. Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)

    PubMed Central

    Price, Trevor D.

    2015-01-01

    Low rates of sequence evolution associated with purifying selection can be interrupted by episodic changes in selective regimes. Visual pigments are a unique system in which we can investigate the functional consequences of genetic changes, therefore connecting genotype to phenotype in the context of natural and sexual selection pressures. We study the RH2 and RH1 visual pigments (opsins) across 22 bird species belonging to two ecologically convergent clades, the New World warblers (Parulidae) and Old World warblers (Phylloscopidae), and evaluate rates of evolution in these clades along with data from 21 additional species. We demonstrate generally slow evolution of these opsins: both Rh1 and Rh2 are highly conserved across Old World and New World warblers. However, Rh2 underwent a burst of evolution within the New World genus Setophaga, where it accumulated substitutions at 6 amino acid sites across the species we studied. Evolutionary analyses revealed a significant increase in dN/dS in Setophaga, implying relatively strong selective pressures to overcome long-standing purifying selection. We studied the effects of each substitution on spectral tuning and found they do not cause large spectral shifts. Thus substitutions may reflect other aspects of opsin function, such as those affecting photosensitivity and/or dark-light adaptation. Although it is unclear what these alterations mean for color perception, we suggest that rapid evolution is linked to sexual selection, given the exceptional plumage colour diversification in Setophaga. PMID:25827331

  11. Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga).

    PubMed

    Bloch, Natasha I; Price, Trevor D; Chang, Belinda S W

    2015-05-01

    Low rates of sequence evolution associated with purifying selection can be interrupted by episodic changes in selective regimes. Visual pigments are a unique system in which we can investigate the functional consequences of genetic changes, therefore connecting genotype to phenotype in the context of natural and sexual selection pressures. We study the RH2 and RH1 visual pigments (opsins) across 22 bird species belonging to two ecologically convergent clades, the New World warblers (Parulidae) and Old World warblers (Phylloscopidae) and evaluate rates of evolution in these clades along with data from 21 additional species. We demonstrate generally slow evolution of these opsins: both Rh1 and Rh2 are highly conserved across Old World and New World warblers. However, Rh2 underwent a burst of evolution within the New World genus Setophaga, where it accumulated substitutions at 6 amino acid sites across the species we studied. Evolutionary analyses revealed a significant increase in dN /dS in Setophaga, implying relatively strong selective pressures to overcome long-standing purifying selection. We studied the effects of each substitution on spectral tuning and found they do not cause large spectral shifts. Thus, substitutions may reflect other aspects of opsin function, such as those affecting photosensitivity and/or dark-light adaptation. Although it is unclear what these alterations mean for colour perception, we suggest that rapid evolution is linked to sexual selection, given the exceptional plumage colour diversification in Setophaga.

  12. Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

    PubMed Central

    Page, Justin T.; Huynh, Mark D.; Liechty, Zach S.; Grupp, Kara; Stelly, David; Hulse, Amanda M.; Ashrafi, Hamid; Van Deynze, Allen; Wendel, Jonathan F.; Udall, Joshua A.

    2013-01-01

    Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton. PMID:23979935

  13. Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences.

    PubMed

    Saber, Morteza Mahmoudi; Adeyemi Babarinde, Isaac; Hettiarachchi, Nilmini; Saitou, Naruya

    2016-07-12

    Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions.

  14. Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores.

    PubMed

    Hoelzel, A R; Lopez, J V; Dover, G A; O'Brien, S J

    1994-08-01

    We describe a repetitive DNA region at the 3' end of the mitochondrial DNA (mtDNA) control region and compare it in 21 carnivore species representing eight carnivore families. The sequence and organization of the repetitive motifs can differ extensively between arrays; however, all motifs appear to be derived from the core motif "ACGT." Sequence data and Southern blot analysis demonstrate extensive heteroplasmy. The general form of the array is similar between heteroplasmic variants within an individual and between individuals within a species (varying primarily in the length of the array, though two clones from the northern elephant seal are exceptional). Within certain families, notably ursids, the array structure is also similar between species. Similarity between species was not apparent in other carnivore families, such as the mustelids, suggesting rapid changes in the organization and sequence of some arrays. The pattern of change seen within and between species suggests that a dominant mechanism involved in the evolution of these arrays is DNA slippage. A comparative analysis shows that the motifs that are being reiterated or deleted vary within and between arrays, suggesting a varying rate of DNA turnover. We discuss the evolutionary implications of the observed patterns of variation and extreme levels of heteroplasmy. PMID:7932782

  15. Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis

    PubMed Central

    Singh, Pushpendra; Benjak, Andrej; Schuenemann, Verena J.; Herbig, Alexander; Avanzi, Charlotte; Busso, Philippe; Nieselt, Kay; Krause, Johannes; Vera-Cabrera, Lucio; Cole, Stewart T.

    2015-01-01

    Mycobacterium lepromatosis is an uncultured human pathogen associated with diffuse lepromatous leprosy and a reactional state known as Lucio's phenomenon. By using deep sequencing with and without DNA enrichment, we obtained the near-complete genome sequence of M. lepromatosis present in a skin biopsy from a Mexican patient, and compared it with that of Mycobacterium leprae, which has undergone extensive reductive evolution. The genomes display extensive synteny and are similar in size (∼3.27 Mb). Protein-coding genes share 93% nucleotide sequence identity, whereas pseudogenes are only 82% identical. The events that led to pseudogenization of 50% of the genome likely occurred before divergence from their most recent common ancestor (MRCA), and both M. lepromatosis and M. leprae have since accumulated new pseudogenes or acquired specific deletions. Functional comparisons suggest that M. lepromatosis has lost several enzymes required for amino acid synthesis whereas M. leprae has a defective heme pathway. M. lepromatosis has retained all functions required to infect the Schwann cells of the peripheral nervous system and therefore may also be neuropathogenic. A phylogeographic survey of 227 leprosy biopsies by differential PCR revealed that 221 contained M. leprae whereas only six, all from Mexico, harbored M. lepromatosis. Phylogenetic comparisons indicate that M. lepromatosis is closer than M. leprae to the MRCA, and a Bayesian dating analysis suggests that they diverged from their MRCA approximately 13.9 Mya. Thus, despite their ancient separation, the two leprosy bacilli are remarkably conserved and still cause similar pathologic conditions. PMID:25831531

  16. Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

    PubMed Central

    Saber, Morteza Mahmoudi; Adeyemi Babarinde, Isaac; Hettiarachchi, Nilmini; Saitou, Naruya

    2016-01-01

    Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions. PMID:27289096

  17. Acceleration and transport of anomalous cosmic rays: Investigating the spectral evolution at Voyager 1 beyond the termination shock

    NASA Astrophysics Data System (ADS)

    Senanayake, Udara K.

    Interstellar neutral atoms entering the heliosphere could become ionized by photo-ionization or charge exchange with solar-wind ions. These newly created ions are picked up by the solar wind and carried to the termination shock (TS) where they are believed to be accelerated by the diffusive shock acceleration process to high energies (˜1-100 MeV n-1). The accelerated ions are known as anomalous cosmic rays (ACRs). When NASA's space probe, Voyager 1 crossed the TS in 2004, the measured ACR spectra did not match the theoretical prediction of a continuous power law, and the source of the high-energy ACRs was not observed. However, over the next few years, in the declining phase of the solar cycle, the spectra began to evolve into the expected power-law profile. The model developed here is based on the suggestion that ACRs are still accelerated at the shock, but away from the Voyager crossing points. First, we study ACR acceleration using a three-dimensional, non-spherical model of the heliosphere that is axisymmetric with respect to the interstellar flow direction. A semi-analytic model of the plasma and magnetic field backgrounds is developed to permit an investigation over a wide range of parameters under controlled conditions. The model is applied to helium ACRs, whose phase-space trajectories are stochastically integrated backward in time until a pre-specified, low-energy boundary of 0.5 MeV n-1, is reached. Next, we propose that the solar cycle had an important effect on the evolving of the spectra in the heliosheath. To investigate this, a magnetohydrodynamic background model with stationary solar-wind inner boundary conditions was used to model the transport of helium and oxygen ions. In addition, we developed a charge consistent stochastic model to simulate multiply charged oxygen ACRs. It is shown that the spectral evolution of ACRs in the heliosheath at Voyager 1 could be explained by combining intermediate-energy particles arriving from the heliotail

  18. Evolution of Group Galaxies from the First Red-Sequence Cluster Survey

    NASA Astrophysics Data System (ADS)

    Li, I. H.; Yee, H. K. C.; Hsieh, B. C.; Gladders, M.

    2012-04-01

    We study the evolution of the red-galaxy fraction (f red) in 905 galaxy groups with 0.15 <= z < 0.52. The galaxy groups are identified by the "probability friends-of-friends" algorithm from the first Red-Sequence Cluster Survey (RCS1) photometric-redshift sample. There is a high degree of uniformity in the properties of the red sequence of the group galaxies, indicating that the luminous red-sequence galaxies in the groups are already in place by z ~ 0.5 and that they have a formation epoch of z >~ 2. In general, groups at lower redshifts exhibit larger f red than those at higher redshifts, showing a group Butcher-Oemler effect. We investigate the evolution of f red by examining its dependence on four parameters, one of which can be classified as intrinsic and three of which can be classified as environmental: galaxy stellar mass (M *), total group stellar mass (M *, grp, a proxy for group halo mass), normalized group-centric radius (r grp), and local galaxy density (Σ5). We find that M * is the dominant parameter such that there is a strong correlation between f red and galaxy stellar mass. Furthermore, the dependence of f red on the environmental parameters is also a strong function of M *. Massive galaxies (M * >~ 1011 M ⊙) show little dependence of f red on r grp, M *, grp, and Σ5 over the redshift range. The dependence of f red on these parameters is primarily seen for galaxies with lower masses, especially for M * <~ 1010.6 M ⊙. We observe an apparent "group down-sizing" effect, in that galaxies in lower-mass halos, after controlling for galaxy stellar mass, have lower f red. We find a dependence of f red on both r grp and Σ5 after the other parameters are controlled. At a fixed r grp, there is a significant dependence of f red on Σ5, while r grp gradients of f red are seen for galaxies in similar Σ5 regions. This indicates that galaxy group environment has a residual effect over that of local galaxy density (or vice versa), and both parameters need

  19. Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution

    SciTech Connect

    Ovcharenko, I; Loots, G; Giardine, B; Hou, M; Ma, J; Hardison, R; Stubbs, L; Miller, W

    2004-07-14

    Multiple sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the tba multi-aligner program for rapid identification of local sequence conservation and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short-and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multi-species comparisons of the GATA3 gene locus and the identification of elements that are conserved differently in avians than in other genomes allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://bio.cse.psu.edu/.

  20. Temporal evolution and electric potential structure of the auroral acceleration region from multispacecraft measurements

    NASA Astrophysics Data System (ADS)

    Forsyth, C.; Fazakerley, A. N.; Walsh, A. P.; Watt, C. E.; Garza, K.; Owen, C. J.; Constantinescu, D. O.; Dandouras, I. S.; Fornacon, K.; Lucek, E. A.; Marklund, G. T.; Sadeghi, S. S.; Khotyaintsev, Y. V.; Masson, A.; Doss, N.

    2013-12-01

    Bright aurorae can be excited by the acceleration of electrons into the atmosphere in violation of ideal magnetohydrodynamics. Modelling studies predict that the accelerating electric potential consists of electric double layers at the boundaries of an acceleration region but observations suggest that particle acceleration occurs throughout this region. Using multispacecraft observations from Cluster, we have examined two upward current regions on 14 December 2009. Our observations show that the potential difference below C4 and C3 changed by up to 1.7 kV between their respective crossings, which were separated by 150 s. The field-aligned current density observed by C3 was also larger than that observed by C4. The potential drop above C3 and C4 was approximately the same in both crossings. Using a novel technique of quantitively comparing the electron spectra measured by Cluster 1 and 3, which were separated in altitude, we determine when these spacecraft made effectively magnetically conjugate observations, and we use these conjugate observations to determine the instantaneous distribution of the potential drop in the AAR. Our observations show that an average of 15% of the potential drop in the AAR was located between C1 at 6235 km and C3 at 4685 km altitude, with a maximum potential drop between the spacecraft of 500 V, and that the majority of the potential drop was below C3. Assuming a spatial invariance along the length of the upward current region, we discuss these observations in terms of temporal changes and the vertical structure of the electrostatic potential drop and in the context of existing models and previous single- and multispacecraft observations.

  1. Temporal evolution and electric potential structure of the auroral acceleration region from multispacecraft measurements

    NASA Astrophysics Data System (ADS)

    Forsyth, C.; Fazakerley, A. N.; Walsh, A. P.; Watt, C. E. J.; Garza, K. J.; Owen, C. J.; Constantinescu, D.; Dandouras, I.; FornaçOn, K.-H.; Lucek, E.; Marklund, G. T.; Sadeghi, S. S.; Khotyaintsev, Y.; Masson, A.; Doss, N.

    2012-12-01

    Bright aurorae can be excited by the acceleration of electrons into the atmosphere in violation of ideal magnetohydrodynamics. Modeling studies predict that the accelerating electric potential consists of electric double layers at the boundaries of an acceleration region but observations suggest that particle acceleration occurs throughout this region. Using multispacecraft observations from Cluster, we have examined two upward current regions on 14 December 2009. Our observations show that the potential difference below C4 and C3 changed by up to 1.7 kV between their respective crossings, which were separated by 150 s. The field-aligned current density observed by C3 was also larger than that observed by C4. The potential drop above C3 and C4 was approximately the same in both crossings. Using a novel technique of quantitively comparing the electron spectra measured by Cluster 1 and 3, which were separated in altitude, we determine when these spacecraft made effectively magnetically conjugate observations, and we use these conjugate observations to determine the instantaneous distribution of the potential drop in the AAR. Our observations show that an average of 15% of the potential drop in the AAR was located between C1 at 6235 km and C3 at 4685 km altitude, with a maximum potential drop between the spacecraft of 500 V, and that the majority of the potential drop was below C3. Assuming a spatial invariance along the length of the upward current region, we discuss these observations in terms of temporal changes and the vertical structure of the electrostatic potential drop and in the context of existing models and previous single- and multispacecraft observations.

  2. Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

    SciTech Connect

    Wu, Xueling; Zhou, Tongqing; Zhu, Jiang; Zhang, Baoshan; Georgiev, Ivelin; Wang, Charlene; Chen, Xuejun; Longo, Nancy S.; Louder, Mark; McKee, Krisha; O’Dell, Sijy; Perfetto, Stephen; Schmidt, Stephen D.; Shi, Wei; Wu, Lan; Yang, Yongping; Yang, Zhi-Yong; Yang, Zhongjia; Zhang, Zhenhai; Bonsignori, Mattia; Crump, John A.; Kapiga, Saidi H.; Sam, Noel E.; Haynes, Barton F.; Simek, Melissa; Burton, Dennis R.; Koff, Wayne C.; Doria-Rose, Nicole A.; Connors, Mark; Mullikin, James C.; Nabel, Gary J.; Roederer, Mario; Shapiro, Lawrence; Kwong, Peter D.; Mascola, John R.

    2013-03-04

    Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.

  3. Pairwise Comparisons of Mitochondrial DNA Sequences in Subdivided Populations and Implications for Early Human Evolution

    PubMed Central

    Marjoram, P.; Donnelly, P.

    1994-01-01

    We consider the effect on the distribution of pairwise differences between mitochondrial DNA sequences of the incorporation into the underlying population genetics model of two particular effects that seem realistic for human populations. The first is that the population size was roughly constant before growing to its current level. The second is that the population is geographically subdivided rather than panmictic. In each case these features tend to encourage multimodal distributions of pairwise differences, in contrast to existing, unimodal datasets. We argue that population genetics models currently used to analyze such data may thus fail to reflect important features of human mitochondrial DNA evolution. These may include selection on the mitochondrial genome, more realistic mutation mechanisms, or special population or migration dynamics. Particularly in view of the variability inherent in the single available human mitochondrial genealogy, it is argued that until these effects are better understood, inferences from such data should be rather cautious. PMID:8150290

  4. The slowly pulsating B-star 18 Pegasi: A testbed for upper main sequence stellar evolution

    NASA Astrophysics Data System (ADS)

    Irrgang, A.; Desphande, A.; Moehler, S.; Mugrauer, M.; Janousch, D.

    2016-06-01

    The predicted width of the upper main sequence in stellar evolution models depends on the empirical calibration of the convective overshooting parameter. Despite decades of discussions, its precise value is still unknown and further observational constraints are required to gauge it. Based on a photometric and preliminary asteroseismic analysis, we show that the mid B-type giant 18 Peg is one of the most evolved members of the rare class of slowly pulsating B-stars and, thus, bears tremendous potential to derive a tight lower limit for the width of the upper main sequence. In addition, 18 Peg turns out to be part of a single-lined spectroscopic binary system with an eccentric orbit that is greater than 6 years. Further spectroscopic and photometric monitoring and a sophisticated asteroseismic investigation are required to exploit the full potential of this star as a benchmark object for stellar evolution theory. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 265.C-5038(A), 069.C-0263(A), and 073.D-0024(A). Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC), proposals H2005-2.2-016 and H2015-3.5-008. Based on observations made with the William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias, proposal W15BN015. Based on observations obtained with telescopes of the University Observatory Jena, which is operated by the Astrophysical Institute of the Friedrich-Schiller-University.

  5. Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication.

    PubMed

    Shi, Tao; Dimitrov, Ivan; Zhang, Yinling; Tax, Frans E; Yi, Jing; Gou, Xiaoping; Li, Jia

    2015-10-01

    Traits related to grain and reproductive organs in grass crops have been under continuous directional selection during domestication. Barley is one of the oldest domesticated crops in human history. Thus genes associated with the grain and reproductive organs in barley may show evidence of dramatic evolutionary change. To understand how artificial selection contributes to protein evolution of biased genes in different barley organs, we used Digital Gene Expression analysis of six barley organs (grain, pistil, anther, leaf, stem and root) to identify genes with biased expression in specific organs. Pairwise comparisons of orthologs between barley and Brachypodium distachyon, as well as between highland and lowland barley cultivars mutually indicated that grain and pistil biased genes show relatively higher protein evolutionary rates compared with the median of all orthologs and other organ biased genes. Lineage-specific protein evolutionary rates estimation showed similar patterns with elevated protein evolution in barley grain and pistil biased genes, yet protein sequences generally evolve much faster in the lowland barley cultivar. Further functional annotations revealed that some of these grain and pistil biased genes with rapid protein evolution are related to nutrient biosynthesis and cell cycle/division. Our analyses provide insights into how domestication differentially shaped the evolution of genes specific to different organs of a crop species, and implications for future functional studies of domestication genes.

  6. Accelerated evolution of sex chromosomes in aphids, an x0 system.

    PubMed

    Jaquiéry, Julie; Stoeckel, Solenn; Rispe, Claude; Mieuzet, Lucie; Legeai, Fabrice; Simon, Jean-Christophe

    2012-02-01

    Sex chromosomes play a role in many important biological processes, including sex determination, genomic conflicts, imprinting, and speciation. In particular, they exhibit several unusual properties such as inheritance pattern, hemizygosity, and reduced recombination, which influence their response to evolutionary factors (e.g., drift, selection, and demography). Here, we examine the evolutionary forces driving X chromosome evolution in aphids, an XO system where females are homozygous (XX) and males are hemizygous (X0) at sex chromosomes. We show by simulations that the unusual mode of transmission of the X chromosome in aphids, coupled with cyclical parthenogenesis, results in similar effective population sizes and predicted levels of genetic diversity for X chromosomes and autosomes under neutral evolution. These results contrast with expectations from standard XX/XY or XX/X0 systems (where the effective population size of the X is three-fourths that of autosomes) and have deep consequences for aphid X chromosome evolution. We then localized 52 microsatellite markers on the X and 351 on autosomes. We genotyped 167 individuals with 356 of these loci and found similar levels of allelic richness on the X and on the autosomes, as predicted by our simulations. In contrast, we detected higher dN and dN/dS ratio for X-linked genes compared with autosomal genes, a pattern compatible with either positive or relaxed selection. Given that both types of chromosomes have similar effective population sizes and that the single copy of the X chromosome of male aphids exposes its recessive genes to selection, some degree of positive selection seems to best explain the higher rates of evolution of X-linked genes. Overall, this study highlights the particular relevance of aphids to study the evolutionary factors driving sex chromosomes and genome evolution.

  7. Evolution of green plants as deduced from 5S rRNA sequences.

    PubMed

    Hori, H; Lim, B L; Osawa, S

    1985-02-01

    We have constructed a phylogenic tree for green plants by comparing 5S rRNA sequences. The tree suggests that the emergence of most of the uni- and multicellular green algae such as Chlamydomonas, Spirogyra, Ulva, and Chlorella occurred in the early stage of green plant evolution. The branching point of Nitella is a little earlier than that of land plants and much later than that of the above green algae, supporting the view that Nitella-like green algae may be the direct precursor to land plants. The Bryophyta and the Pteridophyta separated from each other after emergence of the Spermatophyta. The result is consistent with the view that the Bryophyta evolved from ferns by degeneration. In the Pteridophyta, Psilotum (whisk fern) separated first, and a little later Lycopodium (club moss) separated from the ancestor common to Equisetum (horsetail) and Dryopteris (fern). This order is in accordance with the classical view. During the Spermatophyta evolution, the gymnosperms (Cycas, Ginkgo, and Metasequoia have been studied here) and the angiosperms (flowering plants) separated, and this was followed by the separation of Metasequoia and Cycas (cycad)/Ginkgo (maidenhair tree) on one branch and various flowering plants on the other.

  8. Evolution of green plants as deduced from 5S rRNA sequences

    PubMed Central

    Hori, Hiroshi; Lim, Byung-Lak; Osawa, Syozo

    1985-01-01

    We have constructed a phylogenic tree for green plants by comparing 5S rRNA sequences. The tree suggests that the emergence of most of the uni- and multicellular green algae such as Chlamydomonas, Spirogyra, Ulva, and Chlorella occurred in the early stage of green plant evolution. The branching point of Nitella is a little earlier than that of land plants and much later than that of the above green algae, supporting the view that Nitella-like green algae may be the direct precursor to land plants. The Bryophyta and the Pteridophyta separated from each other after emergence of the Spermatophyta. The result is consistent with the view that the Bryophyta evolved from ferns by degeneration. In the Pteridophyta, Psilotum (whisk fern) separated first, and a little later Lycopodium (club moss) separated from the ancestor common to Equisetum (horsetail) and Dryopteris (fern). This order is in accordance with the classical view. During the Spermatophyta evolution, the gymnosperms (Cycas, Ginkgo, and Metasequoia have been studied here) and the angiosperms (flowering plants) separated, and this was followed by the separation of Metasequoia and Cycas (cycad)/Ginkgo (maidenhair tree) on one branch and various flowering plants on the other. PMID:16593540

  9. Evolution of green plants as deduced from 5S rRNA sequences.

    PubMed

    Hori, H; Lim, B L; Osawa, S

    1985-02-01

    We have constructed a phylogenic tree for green plants by comparing 5S rRNA sequences. The tree suggests that the emergence of most of the uni- and multicellular green algae such as Chlamydomonas, Spirogyra, Ulva, and Chlorella occurred in the early stage of green plant evolution. The branching point of Nitella is a little earlier than that of land plants and much later than that of the above green algae, supporting the view that Nitella-like green algae may be the direct precursor to land plants. The Bryophyta and the Pteridophyta separated from each other after emergence of the Spermatophyta. The result is consistent with the view that the Bryophyta evolved from ferns by degeneration. In the Pteridophyta, Psilotum (whisk fern) separated first, and a little later Lycopodium (club moss) separated from the ancestor common to Equisetum (horsetail) and Dryopteris (fern). This order is in accordance with the classical view. During the Spermatophyta evolution, the gymnosperms (Cycas, Ginkgo, and Metasequoia have been studied here) and the angiosperms (flowering plants) separated, and this was followed by the separation of Metasequoia and Cycas (cycad)/Ginkgo (maidenhair tree) on one branch and various flowering plants on the other. PMID:16593540

  10. A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution.

    PubMed

    Blanquart, Samuel; Lartillot, Nicolas

    2006-11-01

    Variations of nucleotidic composition affect phylogenetic inference conducted under stationary models of evolution. In particular, they may cause unrelated taxa sharing similar base composition to be grouped together in the resulting phylogeny. To address this problem, we developed a nonstationary and nonhomogeneous model accounting for compositional biases. Unlike previous nonstationary models, which are branchwise, that is, assume that base composition only changes at the nodes of the tree, in our model, the process of compositional drift is totally uncoupled from the speciation events. In addition, the total number of events of compositional drift distributed across the tree is directly inferred from the data. We implemented the method in a Bayesian framework, relying on Markov Chain Monte Carlo algorithms, and applied it to several nucleotidic data sets. In most cases, the stationarity assumption was rejected in favor of our nonstationary model. In addition, we show that our method is able to resolve a well-known artifact. By Bayes factor evaluation, we compared our model with 2 previously developed nonstationary models. We show that the coupling between speciations and compositional shifts inherent to branchwise models may lead to an overparameterization, resulting in a lesser fit. In some cases, this leads to incorrect conclusions, concerning the nature of the compositional biases. In contrast, our compound model more flexibly adapts its effective number of parameters to the data sets under investigation. Altogether, our results show that accounting for nonstationary sequence evolution may require more elaborate and more flexible models than those currently used.

  11. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences

    PubMed Central

    Hibbett, David S.; Pine, Elizabeth M.; Langer, Ewald; Langer, Gitta; Donoghue, Michael J.

    1997-01-01

    Homobasidiomycete fungi display many complex fruiting body morphologies, including mushrooms and puffballs, but their anatomical simplicity has confounded efforts to understand the evolution of these forms. We performed a comprehensive phylogenetic analysis of homobasidiomycetes, using sequences from nuclear and mitochondrial ribosomal DNA, with an emphasis on understanding evolutionary relationships of gilled mushrooms and puffballs. Parsimony-based optimization of character states on our phylogenetic trees suggested that strikingly similar gilled mushrooms evolved at least six times, from morphologically diverse precursors. Approximately 87% of gilled mushrooms are in a single lineage, which we call the “euagarics.” Recently discovered 90 million-year-old fossil mushrooms are probably euagarics, suggesting that (i) the origin of this clade must have occurred no later than the mid-Cretaceous and (ii) the gilled mushroom morphology has been maintained in certain lineages for tens of millions of years. Puffballs and other forms with enclosed spore-bearing structures (Gasteromycetes) evolved at least four times. Derivation of Gasteromycetes from forms with exposed spore-bearing structures (Hymenomycetes) is correlated with repeated loss of forcible spore discharge (ballistospory). Diverse fruiting body forms and spore dispersal mechanisms have evolved among Gasteromycetes. Nevertheless, it appears that Hymenomycetes have never been secondarily derived from Gasteromycetes, which suggests that the loss of ballistospory has constrained evolution in these lineages. PMID:9342352

  12. Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

    PubMed

    Tuller, Tamir; Birin, Hadas; Kupiec, Martin; Ruppin, Eytan

    2010-09-01

    The inference of ancestral genomes is a fundamental problem in molecular evolution. Due to the statistical nature of this problem, the most likely or the most parsimonious ancestral genomes usually include considerable error rates. In general, these errors cannot be abolished by utilizing more exhaustive computational approaches, by using longer genomic sequences, or by analyzing more taxa. In recent studies, we showed that co-evolution is an important force that can be used for significantly improving the inference of ancestral genome content. In this work we formally define a computational problem for the inference of ancestral genome content by co-evolution. We show that this problem is NP-hard and hard to approximate and present both a Fixed Parameter Tractable (FPT) algorithm, and heuristic approximation algorithms for solving it. The running time of these algorithms on simulated inputs with hundreds of protein families and hundreds of co-evolutionary relations was fast (up to four minutes) and it achieved an approximation ratio of <1.3. We use our approach to study the ancestral genome content of the Fungi. To this end, we implement our approach on a dataset of 33, 931 protein families and 20, 317 co-evolutionary relations. Our algorithm added and removed hundreds of proteins from the ancestral genomes inferred by maximum likelihood (ML) or maximum parsimony (MP) while slightly affecting the likelihood/parsimony score of the results. A biological analysis revealed various pieces of evidence that support the biological plausibility of the new solutions. In addition, we showed that our approach reconstructs missing values at the leaves of the Fungi evolutionary tree better than ML or MP.

  13. High-throughput sequencing and mutagenesis to accelerate the domestication of Microlaena stipoides as a new food crop.

    PubMed

    Shapter, Frances M; Cross, Michael; Ablett, Gary; Malory, Sylvia; Chivers, Ian H; King, Graham J; Henry, Robert J

    2013-01-01

    Global food demand, climatic variability and reduced land availability are driving the need for domestication of new crop species. The accelerated domestication of a rice-like Australian dryland polyploid grass, Microlaena stipoides (Poaceae), was targeted using chemical mutagenesis in conjunction with high throughput sequencing of genes for key domestication traits. While M. stipoides has previously been identified as having potential as a new grain crop for human consumption, only a limited understanding of its genetic diversity and breeding system was available to aid the domestication process. Next generation sequencing of deeply-pooled target amplicons estimated allelic diversity of a selected base population at 14.3 SNP/Mb and identified novel, putatively mutation-induced polymorphisms at about 2.4 mutations/Mb. A 97% lethal dose (LD₉₇) of ethyl methanesulfonate treatment was applied without inducing sterility in this polyploid species. Forward and reverse genetic screens identified beneficial alleles for the domestication trait, seed-shattering. Unique phenotypes observed in the M2 population suggest the potential for rapid accumulation of beneficial traits without recourse to a traditional cross-breeding strategy. This approach may be applicable to other wild species, unlocking their potential as new food, fibre and fuel crops. PMID:24367532

  14. High-throughput sequencing and mutagenesis to accelerate the domestication of Microlaena stipoides as a new food crop.

    PubMed

    Shapter, Frances M; Cross, Michael; Ablett, Gary; Malory, Sylvia; Chivers, Ian H; King, Graham J; Henry, Robert J

    2013-01-01

    Global food demand, climatic variability and reduced land availability are driving the need for domestication of new crop species. The accelerated domestication of a rice-like Australian dryland polyploid grass, Microlaena stipoides (Poaceae), was targeted using chemical mutagenesis in conjunction with high throughput sequencing of genes for key domestication traits. While M. stipoides has previously been identified as having potential as a new grain crop for human consumption, only a limited understanding of its genetic diversity and breeding system was available to aid the domestication process. Next generation sequencing of deeply-pooled target amplicons estimated allelic diversity of a selected base population at 14.3 SNP/Mb and identified novel, putatively mutation-induced polymorphisms at about 2.4 mutations/Mb. A 97% lethal dose (LD₉₇) of ethyl methanesulfonate treatment was applied without inducing sterility in this polyploid species. Forward and reverse genetic screens identified beneficial alleles for the domestication trait, seed-shattering. Unique phenotypes observed in the M2 population suggest the potential for rapid accumulation of beneficial traits without recourse to a traditional cross-breeding strategy. This approach may be applicable to other wild species, unlocking their potential as new food, fibre and fuel crops.

  15. Accelerated Gene Evolution and Subfunctionalization in thePseudotetraploid Frog Xenopus Laevis

    SciTech Connect

    Hellsten, Uffe; Khokha, Mustafa K.; Grammar, Timothy C.; Harland,Richard M.; Richardson, Paul; Rokhsar, Daniel S.

    2007-03-01

    Ancient whole genome duplications have been implicated in the vertebrate and teleost radiations, and in the emergence of diverse angiosperm lineages, but the evolutionary response to such a perturbation is still poorly understood. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization {approx} 40 million years ago. Analysis of the considerable amount of EST sequence available for this species together with the genome sequence of the related diploid Xenopus tropicalis provides a unique opportunity to study the genomic response to whole genome duplication.

  16. Sequence stratigraphy and evolution of the Antler foreland basin, east-central Nevada

    SciTech Connect

    Trexler, J.H. Jr.; Nitchman, S.P. )

    1990-05-01

    The Mississippian Antler foreland basin contains siliciclastic sedimentary rocks that record a series of orogenic events along the western margin of North America from about 350 to 320 Ma. Our new stratigraphic and sedimentologic studies in Nevada indicate that the strata are not generally progradiational as previously described, and that uplift played a large role in basin evolution. We have recognized three unconformity-bounded stratigraphic sequences in the Antler basin in central Nevada: the Diamond Range submarine-fan system, the Newark Valley fluvial and delta-plain system, and the Green Springs deltaic and shelf-carbonate system. They propose a two-phase history for the antler orogeny: (1) collision of the western edge of North America with the Antler allochthon and downwarping of the continental margin (360-350 Ma), which resulted in deposition of the Diamond Range submarine-fan system; and (2) uplift and low-amplitude folding of the basin (350-320 Ma), accompanied by deposition of a thin veneer of reworked siliciclastic sediments (Newark Valley and Green Springs sequences) across a shallow-marine shelf. Siliciclastic sedimentation waned in the Late Mississippian and Early Pennsylvanian, and gradually gave way to carbonate sedimentation.

  17. Geologic evolution and sequence stratigraphy of the offshore Pelotas Basin, southeast Brazil

    SciTech Connect

    Abreu, V.S.

    1996-12-31

    The Brazilian marginal basins have been studied since the beginning of the 70s. At least nine large basins are distributed along the entire Eastern continental margin. The sedimentary infill of these basins consists of lower Cretaceous (continental/lacustrine) rift section underlying marine upper Cretaceous (carbonate platforms) and marine upper Cretaceous/Tertiary sections, corresponding to the drift phase. The sedimentary deposits are a direct result of the Jurassic to lower Cretaceous break-up of the Pangea. This study will focus on the geologic evolution and sequence stratigraphic analysis of the Pelotas basin (offshore), located in the Southeast portion of the Brazilian continental margin between 28{degrees} and 34{degrees} S, covering approximately 50,000 Km{sup 2}. During the early Cretaceous, when the break-up of the continent began in the south, thick basaltic layers were deposited in the Pelotas basin. These basalts form a thick and broad wedge of dipping seaward reflections interpreted as a transitional crust. During Albian to Turonian times, due to thermal subsidence, an extensive clastic/carbonate platform was developed, in an early drift stage. The sedimentation from the upper Cretaceous to Tertiary was characterized by a predominance of siliciclastics in the southeast margin, marking an accentuate deepening of the basin, showing several cycles related to eustatic fluctuations. Studies have addressed the problems of hydrocarbon exploration in deep water setting within a sequence stratigraphic framework. Thus Pelotas basin can provide a useful analogue for exploration efforts worldwide in offshore passive margins.

  18. Geologic evolution and sequence stratigraphy of the offshore Pelotas Basin, southeast Brazil

    SciTech Connect

    Abreu, V.S. )

    1996-01-01

    The Brazilian marginal basins have been studied since the beginning of the 70s. At least nine large basins are distributed along the entire Eastern continental margin. The sedimentary infill of these basins consists of lower Cretaceous (continental/lacustrine) rift section underlying marine upper Cretaceous (carbonate platforms) and marine upper Cretaceous/Tertiary sections, corresponding to the drift phase. The sedimentary deposits are a direct result of the Jurassic to lower Cretaceous break-up of the Pangea. This study will focus on the geologic evolution and sequence stratigraphic analysis of the Pelotas basin (offshore), located in the Southeast portion of the Brazilian continental margin between 28[degrees] and 34[degrees] S, covering approximately 50,000 Km[sup 2]. During the early Cretaceous, when the break-up of the continent began in the south, thick basaltic layers were deposited in the Pelotas basin. These basalts form a thick and broad wedge of dipping seaward reflections interpreted as a transitional crust. During Albian to Turonian times, due to thermal subsidence, an extensive clastic/carbonate platform was developed, in an early drift stage. The sedimentation from the upper Cretaceous to Tertiary was characterized by a predominance of siliciclastics in the southeast margin, marking an accentuate deepening of the basin, showing several cycles related to eustatic fluctuations. Studies have addressed the problems of hydrocarbon exploration in deep water setting within a sequence stratigraphic framework. Thus Pelotas basin can provide a useful analogue for exploration efforts worldwide in offshore passive margins.

  19. Aging as accelerated accumulation of somatic variants: whole-genome sequencing of centenarian and middle-aged monozygotic twin pairs.

    PubMed

    Ye, Kai; Beekman, Marian; Lameijer, Eric-Wubbo; Zhang, Yanju; Moed, Matthijs H; van den Akker, Erik B; Deelen, Joris; Houwing-Duistermaat, Jeanine J; Kremer, Dennis; Anvar, Seyed Yahya; Laros, Jeroen F J; Jones, David; Raine, Keiran; Blackburne, Ben; Potluri, Shobha; Long, Quan; Guryev, Victor; van der Breggen, Ruud; Westendorp, Rudi G J; 't Hoen, Peter A C; den Dunnen, Johan; van Ommen, Gert Jan B; Willemsen, Gonneke; Pitts, Steven J; Cox, David R; Ning, Zemin; Boomsma, Dorret I; Slagboom, P Eline

    2013-12-01

    It has been postulated that aging is the consequence of an accelerated accumulation of somatic DNA mutations and that subsequent errors in the primary structure of proteins ultimately reach levels sufficient to affect organismal functions. The technical limitations of detecting somatic changes and the lack of insight about the minimum level of erroneous proteins to cause an error catastrophe hampered any firm conclusions on these theories. In this study, we sequenced the whole genome of DNA in whole blood of two pairs of monozygotic (MZ) twins, 40 and 100 years old, by two independent next-generation sequencing (NGS) platforms (Illumina and Complete Genomics). Potentially discordant single-base substitutions supported by both platforms were validated extensively by Sanger, Roche 454, and Ion Torrent sequencing. We demonstrate that the genomes of the two twin pairs are germ-line identical between co-twins, and that the genomes of the 100-year-old MZ twins are discerned by eight confirmed somatic single-base substitutions, five of which are within introns. Putative somatic variation between the 40-year-old twins was not confirmed in the validation phase. We conclude from this systematic effort that by using two independent NGS platforms, somatic single nucleotide substitutions can be detected, and that a century of life did not result in a large number of detectable somatic mutations in blood. The low number of somatic variants observed by using two NGS platforms might provide a framework for detecting disease-related somatic variants in phenotypically discordant MZ twins. PMID:24182360

  20. Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

    PubMed Central

    Axelsen, Jacob Bock; Yan, Koon-Kiu; Maslov, Sergei

    2007-01-01

    Background The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic parameters of these three basic processes is contained in the proteome-wide distribution of sequence identities of pairs of paralogous proteins. Results We introduce a simple mathematical framework based on a stochastic birth-and-death model that allows one to extract some of this information and apply it to the set of all pairs of paralogous proteins in H. pylori, E. coli, S. cerevisiae, C. elegans, D. melanogaster, and H. sapiens. It was found that the histogram of sequence identities p generated by an all-to-all alignment of all protein sequences encoded in a genome is well fitted with a power-law form ~ p-γ with the value of the exponent γ around 4 for the majority of organisms used in this study. This implies that the intra-protein variability of substitution rates is best described by the Gamma-distribution with the exponent α ≈ 0.33. Different features of the shape of such histograms allow us to quantify the ratio between the genome-wide average deletion/duplication rates and the amino-acid substitution rate. Conclusion We separately measure the short-term ("raw") duplication and deletion rates rdup∗, rdel∗ which include gene copies that will be removed soon after the duplication event and their dramatically reduced long-term counterparts rdup, rdel. High deletion rate among recently duplicated proteins is consistent with a scenario in which they didn't have enough time to significantly change their functional roles and thus are to a large degree disposable. Systematic trends of each of the four duplication/deletion rates with the total number of genes in the genome were analyzed. All but the deletion rate of recent duplicates rdel∗ were shown to systematically increase with Ngenes. Abnormally flat shapes

  1. Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism

    NASA Technical Reports Server (NTRS)

    Nakayama, S.; Kretsinger, R. H.

    1993-01-01

    In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

  2. Pulse evolution and plasma-wave phase velocity in channel-guided laser-plasma accelerators.

    PubMed

    Benedetti, C; Rossi, F; Schroeder, C B; Esarey, E; Leemans, W P

    2015-08-01

    The self-consistent laser evolution of an intense, short-pulse laser exciting a plasma wave and propagating in a preformed plasma channel is investigated, including the effects of pulse steepening and energy depletion. In the weakly relativistic laser intensity regime, analytical expressions for the laser energy depletion, pulse self-steepening rate, laser intensity centroid velocity, and phase velocity of the plasma wave are derived and validated numerically. PMID:26382537

  3. Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat is not only an important crop but also an excellent plant species for nuclear mitochondrial interaction studies. To investigate the level of sequence changes introduced into the mitochondrial genome under the alloplasmic conditions, three mitochondrial genomes of Triticum-Aegilops species w...

  4. A Space-Time Process Model for the Evolution of DNA Sequences

    PubMed Central

    Yang, Z.

    1995-01-01

    We describe a model for the evolution of DNA sequences by nucleotide substitution, whereby nucleotide sites in the sequence evolve over time, whereas the rates of substitution are variable and correlated over sites. The temporal process used to describe substitutions between nucleotides is a continuous-time Markov process, with the four nucleotides as the states. The spatial process used to describe variation and dependence of substitution rates over sites is based on a serially correlated gamma distribution, i.e., an auto-gamma model assuming Markov-dependence of rates at adjacent sites. To achieve computational efficiency, we use several equal-probability categories to approximate the gamma distribution, and the result is an auto-discrete-gamma model for rates over sites. Correlation of rates at sites then is modeled by the Markov chain transition of rates at adjacent sites from one rate category to another, the states of the chain being the rate categories. Two versions of nonparametric models, which place no restrictions on the distributional forms of rates for sites, also are considered, assuming either independence or Markov dependence. The models are applied to data of a segment of mitochondrial genome from nine primate species. Model parameters are estimated by the maximum likelihood method, and models are compared by the likelihood ratio test. Tremendous variation of rates among sites in the sequence is revealed by the analyses, and when rate differences for different codon positions are appropriately accounted for in the models, substitution rates at adjacent sites are found to be strongly (positively) correlated. Robustness of the results to uncertainty of the phylogenetic tree linking the species is examined. PMID:7713447

  5. ECHO Project: a series of tools for studying and characterizing seismic sequences evolution

    NASA Astrophysics Data System (ADS)

    Falcone, Giuseppe; De Santis, Angelo; Di Giovambattista, Rita; Cianchini, Gianfranco; Murru, Maura; Calderoni, Giovanna; Lucente, Pio Francesco; De Gori, Pasquale; Frepoli, Alberto; Signanini, Patrizio; Rainone, Mario; Vessia, Giovanna

    2016-04-01

    One of the most ubiquitous problems in seismology is to discriminate between seismic sequences (a series of small-to-moderate earthquakes that culminate with a mainshock) and swarms (diffuse seismicity w/o mainshock), that can be easily done only after a certain class of earthquakes have occurred. We propose to put these phenomena under the same framework provided by the geosystemics (De Santis, 2009, 2014), where the planet Earth and its processes are seen from a holistic point of view, and the New Geophysics (Crampin et al., 2013), where fluid-saturated microcracks in almost all crustal rocks are so closely-spaced they verge on failure and hence are highly-compliant critical systems (Signanini and De Santis, 2012). In this context, nonlinear concepts typical of Chaos and Information theories are fundamental to study and characterize the various features of the series of seismic events, and, eventually, to discriminate between seismic sequences and swarms. The two theories imply the use of non-linear techniques which are innovative in seismology. The project ECHO ("Entropy and CHaOs: tools for studying and characterizing seismic sequences evolution"), a recent INGV-funded project, would aim at applying the above approaches in a more integrated way mainly to establish a suite of effective tools to disclose and characterise the principal features of the series of earthquakes which are of interest. In our view this will represent the very first step before to face the more challenging (but longer-term) problem of discriminating between the two kinds of series of seismic events. This poster will describe these kinds of preliminary activities and relative results in the framework of the project.

  6. Future evolution and finite-time singularities in F(R) gravity unifying inflation and cosmic acceleration

    SciTech Connect

    Nojiri, Shin'ichi; Odintsov, Sergei D.

    2008-08-15

    We study the future evolution of quintessence/phantom-dominated epoch in modified F(R) gravity which unifies the early-time inflation with late-time acceleration and which is consistent with observational tests. Using the reconstruction technique it is demonstrated that there are models where any known (big rip, II, III, or IV type) singularity may classically occur. From another side, in Einstein frame (scalar-tensor description) only IV type singularity occurs. Near the singularity the classical description breaks up, and it is demonstrated that quantum effects act against the singularity and may prevent its appearance. The realistic F(R) gravity which is future singularity free is proposed. We point out that additional modification of any F(R) gravity by the terms relevant at the early universe is possible, in such a way that future singularity does not occur even classically.

  7. Nonlinear Evolution of a 3D Inertial Alfvén Wave and Its Implication in Particle Acceleration

    NASA Astrophysics Data System (ADS)

    Sharma, Prachi; Yadav, Nitin; Sharma, R. P.

    2016-03-01

    A simulation based on a pseudo-spectral method has been performed in order to study particle acceleration. A model for the acceleration of charged particles by field localization is developed for the low-β plasma. For this purpose, a fractional diffusion approach has been employed. The nonlinear interaction between a 3D inertial Alfvén wave and a slow magnetosonic wave has been examined, and the dynamical equations of these two waves in the presence of ponderomotive nonlinearity have been solved numerically. The nonlinear evolution of the inertial Alfvén wave in the presence of slow magnetosonic wave undergoes a filamentation instability and results in field intensity localization. The results obtained show the localization and power spectrum of inertial Alfvén wave due to nonlinear coupling. The scaling obtained after the first break point of the magnetic power spectrum has been used to calculate the formation of the thermal tail of energetic particles in the solar corona.

  8. Collective properties of injection-induced earthquake sequences: 2. Spatiotemporal evolution and magnitude frequency distributions

    NASA Astrophysics Data System (ADS)

    Dempsey, David; Suckale, Jenny; Huang, Yihe

    2016-05-01

    Probabilistic seismic hazard assessment for induced seismicity depends on reliable estimates of the locations, rate, and magnitude frequency properties of earthquake sequences. The purpose of this paper is to investigate how variations in these properties emerge from interactions between an evolving fluid pressure distribution and the mechanics of rupture on heterogeneous faults. We use an earthquake sequence model, developed in the first part of this two-part series, that computes pore pressure evolution, hypocenter locations, and rupture lengths for earthquakes triggered on 1-D faults with spatially correlated shear stress. We first consider characteristic features that emerge from a range of generic injection scenarios and then focus on the 2010-2011 sequence of earthquakes linked to wastewater disposal into two wells near the towns of Guy and Greenbrier, Arkansas. Simulations indicate that one reason for an increase of the Gutenberg-Richter b value for induced earthquakes is the different rates of reduction of static and residual strength as fluid pressure rises. This promotes fault rupture at lower stress than equivalent tectonic events. Further, b value is shown to decrease with time (the induced seismicity analog of b value reduction toward the end of the seismic cycle) and to be higher on faults with lower initial shear stress. This suggests that faults in the same stress field that have different orientations, and therefore different levels of resolved shear stress, should exhibit seismicity with different b-values. A deficit of large-magnitude events is noted when injection occurs directly onto a fault and this is shown to depend on the geometry of the pressure plume. Finally, we develop models of the Guy-Greenbrier sequence that captures approximately the onset, rise and fall, and southwest migration of seismicity on the Guy-Greenbrier fault. Constrained by the migration rate, we estimate the permeability of a 10 m thick critically stressed basement

  9. Community-level education accelerates the cultural evolution of fertility decline.

    PubMed

    Colleran, Heidi; Jasienska, Grazyna; Nenko, Ilona; Galbarczyk, Andrzej; Mace, Ruth

    2014-03-22

    Explaining why fertility declines as populations modernize is a profound theoretical challenge. It remains unclear whether the fundamental drivers are economic or cultural in nature. Cultural evolutionary theory suggests that community-level characteristics, for example average education, can alter how low-fertility preferences are transmitted and adopted. These assumptions have not been empirically tested. Here, we show that community-level education accelerates fertility decline in a way that is neither predicted by individual characteristics, nor by the level of economic modernization in a population. In 22 high-fertility communities in Poland, fertility converged on a smaller family size as average education in the community increased-indeed community-level education had a larger impact on fertility decline than did individual education. This convergence was not driven by educational levels being more homogeneous, but by less educated women having fewer children than expected, and more highly educated social networks, when living among more highly educated neighbours. The average level of education in a community may influence the social partners women interact with, both within and beyond their immediate social environments, altering the reproductive norms they are exposed to. Given a critical mass of highly educated women, less educated neighbours may adopt their reproductive behaviour, accelerating the pace of demographic transition. Individual characteristics alone cannot capture these dynamics and studies relying solely on them may systematically underestimate the importance of cultural transmission in driving fertility declines. Our results are inconsistent with a purely individualistic, rational-actor model of fertility decline and suggest that optimization of reproduction is partly driven by cultural dynamics beyond the individual.

  10. Fractography evolution in accelerated aging of UHMWPE after gamma irradiation in air.

    PubMed

    Medel, F; Gómez-Barrena, E; García-Alvarez, F; Ríos, R; Gracia-Villa, L; Puértolas, J A

    2004-01-01

    We studied the fracture surface evolution of ultra high molecular weight polyethylene (UHMWPE) specimens, manufactured from GUR 1050 compression moulded sheets, after gamma sterilisation in air followed by different aging times after thermal treatment at 120 degrees C. Degradation profiles were obtained by FTIR and DSC measurements after 0, 7, 14, 24 and 36h aging. We observed by SEM the morphology patterns at these aging times, in surface fractographies after uniaxial tensile test of standardised samples. The results pointed out clear differences between short and long aging times. At shorter times, 7h, the behaviour was similar to non-degraded UHMWPE, exhibiting ductile behaviour. At longer times, 24-36h, this thermal protocol provided a highly degraded zone in the subsurface, similar to the white band found after gamma irradiation in air followed by natural aging, although closer to the surface, at 150-200mum. The microstructure of this oxidation zone, similarly found in gamma irradiated samples shelf-aged for 6-7 years, although with different distribution of microvoids, was formed by fibrils, associated with embrittlement of the oxidised UHMWPE. In addition, the evolution of the oxidation index, the enthalpy content, the mechanical parameters, and the depth of the oxidation front deduced from the fractographies versus aging time showed that a changing behaviour in the degradation rate appeared at intermediate aging times.

  11. Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling

    SciTech Connect

    Vrugt, Jasper A; Hyman, James M; Robinson, Bruce A; Higdon, Dave; Ter Braak, Cajo J F; Diks, Cees G H

    2008-01-01

    Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.

  12. EVOLUTION OF GROUP GALAXIES FROM THE FIRST RED-SEQUENCE CLUSTER SURVEY

    SciTech Connect

    Li, I. H.; Yee, H. K. C.; Hsieh, B. C.; Gladders, M. E-mail: hyee@astro.utoronto.ca E-mail: gladders@oddjob.uchicago.edu

    2012-04-20

    We study the evolution of the red-galaxy fraction (f{sub red}) in 905 galaxy groups with 0.15 {<=} z < 0.52. The galaxy groups are identified by the 'probability friends-of-friends' algorithm from the first Red-Sequence Cluster Survey (RCS1) photometric-redshift sample. There is a high degree of uniformity in the properties of the red sequence of the group galaxies, indicating that the luminous red-sequence galaxies in the groups are already in place by z {approx} 0.5 and that they have a formation epoch of z {approx}> 2. In general, groups at lower redshifts exhibit larger f{sub red} than those at higher redshifts, showing a group Butcher-Oemler effect. We investigate the evolution of f{sub red} by examining its dependence on four parameters, one of which can be classified as intrinsic and three of which can be classified as environmental: galaxy stellar mass (M{sub *}), total group stellar mass (M{sub *,grp}, a proxy for group halo mass), normalized group-centric radius (r{sub grp}), and local galaxy density ({Sigma}{sub 5}). We find that M{sub *} is the dominant parameter such that there is a strong correlation between f{sub red} and galaxy stellar mass. Furthermore, the dependence of f{sub red} on the environmental parameters is also a strong function of M{sub *}. Massive galaxies (M{sub *} {approx}> 10{sup 11} M{sub Sun }) show little dependence of f{sub red} on r{sub grp}, M{sub *,grp}, and {Sigma}{sub 5} over the redshift range. The dependence of f{sub red} on these parameters is primarily seen for galaxies with lower masses, especially for M{sub *} {approx}< 10{sup 10.6} M{sub Sun }. We observe an apparent 'group down-sizing' effect, in that galaxies in lower-mass halos, after controlling for galaxy stellar mass, have lower f{sub red}. We find a dependence of f{sub red} on both r{sub grp} and {Sigma}{sub 5} after the other parameters are controlled. At a fixed r{sub grp}, there is a significant dependence of f{sub red} on {Sigma}{sub 5}, while r{sub grp

  13. A multilocus phylogeny of the desmid genus Micrasterias (Streptophyta): evidence for the accelerated rate of morphological evolution in protists.

    PubMed

    Škaloud, Pavel; Nemjová, Katarína; Veselá, Jana; Černá, Kateřina; Neustupa, Jiří

    2011-12-01

    Micrasterias, the name of which is derived from the Greek for 'little star', comprises possibly the most spectacularly shaped desmids (Desmidiales, Streptophyta). Presently, the genus Micrasterias includes about 60 traditional species, the majority of which were described in the early 19th century. We used a comprehensive multigene dataset (including SSU rDNA, psaA, and coxIII loci) of 34 Micrasterias taxa to assess the relationships between individual morphological species. The resulting phylogeny was used to assess the patterns characterizing the morphological evolution of this genus. The phylogenetic analysis led to the recognition of eight well-resolved lineages that could be characterized by selected morphological features. Apart from the members of Micrasterias, three species belonged to different traditional desmid genera (Cosmarium, Staurodesmus, and Triploceras) and were inferred to be nested within the genus. Morphological comparisons of these species with their relatives revealed an accelerated rate of morphological evolution. Mapping morphological diversification of the genus on the phylogenetic tree revealed profound differences in the phylogenetic signal of selected phenotypic features. Whereas the branching pattern of the cells clearly correlated with the phylogeny, cell complexity possibly reflected rather their adaptive morphological responses to environmental conditions. Finally, ancestral reconstruction of distribution patterns indicated potential origin of the genus in North America, with additional speciation events occurring in the Indo-Malaysian region.

  14. The evolution of proteins from random amino acid sequences: II. Evidence from the statistical distributions of the lengths of modern protein sequences.

    PubMed

    White, S H

    1994-04-01

    entirely consistent with the observations of Brown et al. (1990a,b, Nucleic Acids Res 18:2079-2086 and 18: 6339-6345) which show that tetra-nucleotides (stop codon plus following nucleotide) are the actual signals for termination of translation in both prokaryotes and eukaryotes. Second, the strong dependence of statistical length distributions on sequence-termination signaling codes implies that the evolution of stop codons and translation-termination processes was as important as gene splicing in early evolution. Third, because the theory is based upon a simple no-exon stochastic model, it provides a plausible alternative to a limited universe of exons from which all proteins evolved by gene duplication and exon splicing (Dorit et al. 1990, Science 250:1377-1382).

  15. Conservation of Plastid Sequences in the Plant Nuclear Genome for Millions of Years Facilitates Endosymbiotic Evolution1[W][OA

    PubMed Central

    Rousseau-Gueutin, Mathieu; Ayliffe, Michael A.; Timmis, Jeremy N.

    2011-01-01

    The nuclear genome of eukaryotes contains large amounts of cytoplasmic organelle DNA (nuclear integrants of organelle DNA [norgs]). The recent sequencing of many mitochondrial and chloroplast genomes has enabled investigation of the potential role of norgs in endosymbiotic evolution. In this article, we describe a new polymerase chain reaction-based method that allows the identification and evolutionary study of recent and older norgs in a range of eukaryotes. We tested this method in the genus Nicotiana and obtained sequences from seven nuclear integrants of plastid DNA (nupts) totaling 25 kb in length. These nupts were estimated to have been transferred 0.033 to 5.81 million years ago. The spectrum of mutations present in the potential protein-coding sequences compared with the noncoding sequences of each nupt revealed that nupts evolve in a nuclear-specific manner and are under neutral evolution. Indels were more frequent in noncoding regions than in potential coding sequences of former chloroplastic DNA, most probably due to the presence of a higher number of homopolymeric sequences. Unexpectedly, some potential protein-coding sequences within the nupts still contained intact open reading frames for up to 5.81 million years. These results suggest that chloroplast genes transferred to the nucleus have in some cases several millions of years to acquire nuclear regulatory elements and become functional. The different factors influencing this time frame and the potential role of nupts in endosymbiotic gene transfer are discussed. PMID:22034627

  16. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.

    PubMed

    Zhang, Tongwu; Fang, Yongjun; Wang, Xumin; Deng, Xin; Zhang, Xiaowei; Hu, Songnian; Yu, Jun

    2012-01-01

    The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage. PMID:22291979

  17. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.

    PubMed

    Zhang, Tongwu; Fang, Yongjun; Wang, Xumin; Deng, Xin; Zhang, Xiaowei; Hu, Songnian; Yu, Jun

    2012-01-01

    The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage.

  18. Confronting uncertainties in stellar physics. II. Exploring differences in main-sequence stellar evolution tracks

    NASA Astrophysics Data System (ADS)

    Stancliffe, R. J.; Fossati, L.; Passy, J.-C.; Schneider, F. R. N.

    2016-02-01

    We assess the systematic uncertainties in stellar evolutionary calculations for low- to intermediate-mass, main-sequence stars. We compare published stellar tracks from several different evolution codes with our own tracks computed using the stellar codes stars and mesa. In particular, we focus on tracks of 1 and 3 M⊙ at solar metallicity. We find that the spread in the available 1 M⊙ tracks (computed before the recent solar composition revision) can be covered by tracks between 0.97-1.01 M⊙ computed with the stars code. We assess some possible causes of the origin of this uncertainty, including how the choice of input physics and the solar constraints used to perform the solar calibration affect the tracks. We find that for a 1 M⊙ track, uncertainties of around 10% in the initial hydrogen abundance and initial metallicity produce around a 2% error in mass. For the 3 M⊙ tracks, there is very little difference between the tracks from the various different stellar codes. The main difference comes in the extent of the main sequence, which we believe results from the different choices of the implementation of convective overshooting in the core. Uncertainties in the initial abundances lead to a 1-2% error in the mass determination. These uncertainties cover only part of the total error budget, which should also include uncertainties in the input physics (e.g., reaction rates, opacities, convective models) and any missing physics (e.g., radiative levitation, rotation, magnetic fields). Uncertainties in stellar surface properties such as luminosity and effective temperature will further reduce the accuracy of any potential mass determinations.

  19. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.

    PubMed

    Orlando, Ludovic; Ginolhac, Aurélien; Zhang, Guojie; Froese, Duane; Albrechtsen, Anders; Stiller, Mathias; Schubert, Mikkel; Cappellini, Enrico; Petersen, Bent; Moltke, Ida; Johnson, Philip L F; Fumagalli, Matteo; Vilstrup, Julia T; Raghavan, Maanasa; Korneliussen, Thorfinn; Malaspinas, Anna-Sapfo; Vogt, Josef; Szklarczyk, Damian; Kelstrup, Christian D; Vinther, Jakob; Dolocan, Andrei; Stenderup, Jesper; Velazquez, Amhed M V; Cahill, James; Rasmussen, Morten; Wang, Xiaoli; Min, Jiumeng; Zazula, Grant D; Seguin-Orlando, Andaine; Mortensen, Cecilie; Magnussen, Kim; Thompson, John F; Weinstock, Jacobo; Gregersen, Kristian; Røed, Knut H; Eisenmann, Véra; Rubin, Carl J; Miller, Donald C; Antczak, Douglas F; Bertelsen, Mads F; Brunak, Søren; Al-Rasheid, Khaled A S; Ryder, Oliver; Andersson, Leif; Mundy, John; Krogh, Anders; Gilbert, M Thomas P; Kjær, Kurt; Sicheritz-Ponten, Thomas; Jensen, Lars Juhl; Olsen, Jesper V; Hofreiter, Michael; Nielsen, Rasmus; Shapiro, Beth; Wang, Jun; Willerslev, Eske

    2013-07-01

    The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.

  20. The evolution of angular momentum among zero-age main-sequence solar-type stars

    NASA Technical Reports Server (NTRS)

    Soderblom, David R.; Stauffer, John R.; Macgregor, Keith B.; Jones, Burton F.

    1993-01-01

    We consider a survey of rotation among F, G, and K dwarfs of the Pleiades in the context of other young clusters (Alpha Persei and the Hyades) and pre-main-sequence (PMS) stars (in Taurus-Auriga and Orion) in order to examine how the angular momentum of a star like the sun evolves during its early life on the main sequence. The rotation of PMS stars can be evolved into distributions like those seen in the young clusters if there is only modest, rotation-independent angular momentum loss prior to the ZAMS. Even then, the ultrafast rotators (UFRs, or ZAMS G and K dwarfs with v sin i equal to or greater than 30 km/s) must owe their extra angular momentum to their conditions of formation and to different angular momentum loss rates above a threshold velocity, for it is unlikely that these stars had angular momentum added as they neared the ZAMS, nor can a spread in ages within a cluster account for the range of rotation seen. Only a fraction of solar-type stars are thus capable of becoming UFRs, and it is not a phase that all stars experience. Simple scaling relations (like the Skumanich relation) applied to the observed surface rotation rates of young solar-type stars cannot reproduce the way in which the Pleiades evolve into the Hyades. We argue that invoking internal differential rotation in these ZAMS stars can explain several aspects of the observations and thus can provide a consistent picture of ZAMS angular momentum evolution.

  1. Polyphyly and convergent morphological evolution in Commelinales and Commelinidae: evidence from rbcL sequence data.

    PubMed

    Givnish, T J; Evans, T M; Pires, J C; Sytsma, K J

    1999-08-01

    speciation, such as restricted seed dispersal (especially in forest interior groups with fleshy fruits), polyploidy, aneuploidy, and apomixis. Species diversity is unrelated to the rate/amount of rbcL sequence evolution.

  2. Dissecting the roles of local packing density and longer-range effects in protein sequence evolution.

    PubMed

    Shahmoradi, Amir; Wilke, Claus O

    2016-06-01

    What are the structural determinants of protein sequence evolution? A number of site-specific structural characteristics have been proposed, most of which are broadly related to either the density of contacts or the solvent accessibility of individual residues. Most importantly, there has been disagreement in the literature over the relative importance of solvent accessibility and local packing density for explaining site-specific sequence variability in proteins. We show that this discussion has been confounded by the definition of local packing density. The most commonly used measures of local packing, such as contact number and the weighted contact number, represent the combined effects of local packing density and longer-range effects. As an alternative, we propose a truly local measure of packing density around a single residue, based on the Voronoi cell volume. We show that the Voronoi cell volume, when calculated relative to the geometric center of amino-acid side chains, behaves nearly identically to the relative solvent accessibility, and each individually can explain, on average, approximately 34% of the site-specific variation in evolutionary rate in a data set of 209 enzymes. An additional 10% of variation can be explained by nonlocal effects that are captured in the weighted contact number. Consequently, evolutionary variation at a site is determined by the combined effects of the immediate amino-acid neighbors of that site and effects mediated by more distant amino acids. We conclude that instead of contrasting solvent accessibility and local packing density, future research should emphasize on the relative importance of immediate contacts and longer-range effects on evolutionary variation. Proteins 2016; 84:841-854. © 2016 Wiley Periodicals, Inc. PMID:26990194

  3. EVOLUTION OF COLD STREAMS AND THE EMERGENCE OF THE HUBBLE SEQUENCE

    SciTech Connect

    Cen, Renyue

    2014-07-01

    A new physical framework for the emergence of the Hubble sequence is outlined, based on novel analyses performed to quantify the evolution of cold streams of a large sample of galaxies from a state-of-the-art ultra-high resolution, large-scale adaptive mesh-refinement hydrodynamic simulation in a fully cosmological setting. It is found that the following three key physical variables of galactic cold inflows crossing the virial sphere substantially decrease with decreasing redshift: the number of streams N {sub 90} that make up 90% of concurrent inflow mass flux, average inflow rate per stream M-dot {sub 90} and mean (mass flux weighted) gas density in the streams n {sub gas}. Another key variable, the stream dimensionless angular momentum parameter λ, is found to instead increase with decreasing redshift. Assimilating these trends and others naturally leads to a physically coherent scenario for the emergence of the Hubble sequence, including the following expectations: (1) the predominance of a mixture of disproportionately small irregular and complex disk galaxies at z ≥ 2 when most galaxies have multiple concurrent streams, (2) the beginning of the appearance of flocculent spirals at z ∼ 1-2 when the number of concurrent streams are about 2-3, (3) the grand-design spiral galaxies appear at z ≤ 1 when galaxies with only one major cold stream significantly emerge. These expected general trends are in good accord with observations. Early-type galaxies are those that have entered a perennial state of zero cold gas stream, with their abundance increasing with decreasing redshift.

  4. Evolution on neutral networks accelerates the ticking rate of the molecular clock.

    PubMed

    Manrubia, Susanna; Cuesta, José A

    2015-01-01

    Large sets of genotypes give rise to the same phenotype, because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as the genotype mutates into another one on the same set. By linking every pair of genotypes that are mutually accessible through mutation, genotypes organize themselves into neutral networks (NNs). These networks are known to be heterogeneous and assortative, and these properties affect the evolutionary dynamics of the population. By studying the dynamics of populations on NNs with arbitrary topology, we analyse the effect of assortativity, of NN (phenotype) fitness and of network size. We find that the probability that the population leaves the network is smaller the longer the time spent on it. This progressive 'phenotypic entrapment' entails a systematic increase in the overdispersion of the process with time and an acceleration in the fixation rate of neutral mutations. We also quantify the variation of these effects with the size of the phenotype and with its fitness relative to that of neighbouring alternatives.

  5. Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene

    PubMed Central

    Schobel, Seth A.; Stucker, Karla M.; Moore, Martin L.; Anderson, Larry J.; Larkin, Emma K.; Shankar, Jyoti; Bera, Jayati; Puri, Vinita; Shilts, Meghan H.; Rosas-Salazar, Christian; Halpin, Rebecca A.; Fedorova, Nadia; Shrivastava, Susmita; Stockwell, Timothy B.; Peebles, R. Stokes; Hartert, Tina V.; Das, Suman R.

    2016-01-01

    Respiratory Syncytial Virus (RSV) is responsible for considerable morbidity and mortality worldwide and is the most important respiratory viral pathogen in infants. Extensive sequence variability within and between RSV group A and B viruses and the ability of multiple clades and sub-clades of RSV to co-circulate are likely mechanisms contributing to the evasion of herd immunity. Surveillance and large-scale whole-genome sequencing of RSV is currently limited but would help identify its evolutionary dynamics and sites of selective immune evasion. In this study, we performed complete-genome next-generation sequencing of 92 RSV isolates from infants in central Tennessee during the 2012–2014 RSV seasons. We identified multiple co-circulating clades of RSV from both the A and B groups. Each clade is defined by signature N- and O-linked glycosylation patterns. Analyses of specific RSV genes revealed high rates of positive selection in the attachment (G) gene. We identified RSV-A viruses in circulation with and without a recently reported 72-nucleotide G gene sequence duplication. Furthermore, we show evidence of convergent evolution of G gene sequence duplication and fixation over time, which suggests a potential fitness advantage of RSV with the G sequence duplication. PMID:27212633

  6. Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene.

    PubMed

    Schobel, Seth A; Stucker, Karla M; Moore, Martin L; Anderson, Larry J; Larkin, Emma K; Shankar, Jyoti; Bera, Jayati; Puri, Vinita; Shilts, Meghan H; Rosas-Salazar, Christian; Halpin, Rebecca A; Fedorova, Nadia; Shrivastava, Susmita; Stockwell, Timothy B; Peebles, R Stokes; Hartert, Tina V; Das, Suman R

    2016-01-01

    Respiratory Syncytial Virus (RSV) is responsible for considerable morbidity and mortality worldwide and is the most important respiratory viral pathogen in infants. Extensive sequence variability within and between RSV group A and B viruses and the ability of multiple clades and sub-clades of RSV to co-circulate are likely mechanisms contributing to the evasion of herd immunity. Surveillance and large-scale whole-genome sequencing of RSV is currently limited but would help identify its evolutionary dynamics and sites of selective immune evasion. In this study, we performed complete-genome next-generation sequencing of 92 RSV isolates from infants in central Tennessee during the 2012-2014 RSV seasons. We identified multiple co-circulating clades of RSV from both the A and B groups. Each clade is defined by signature N- and O-linked glycosylation patterns. Analyses of specific RSV genes revealed high rates of positive selection in the attachment (G) gene. We identified RSV-A viruses in circulation with and without a recently reported 72-nucleotide G gene sequence duplication. Furthermore, we show evidence of convergent evolution of G gene sequence duplication and fixation over time, which suggests a potential fitness advantage of RSV with the G sequence duplication. PMID:27212633

  7. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

    PubMed Central

    2011-01-01

    Background We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Conclusions Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. PMID:21854559

  8. Virus evolution during chronic hepatitis B virus infection as revealed by ultradeep sequencing data.

    PubMed

    Jones, Leandro R; Sede, Mariano; Manrique, Julieta M; Quarleri, Jorge

    2016-02-01

    Despite chronic hepatitis B virus (HBV) infection (CHB) being a leading cause of liver cirrhosis and cancer, HBV evolution during CHB is not fully understood. Recent studies have indicated that virus diversity progressively increases along the course of CHB and that some virus mutations correlate with severe liver conditions such as chronic hepatitis, cirrhosis and hepatocellular carcinoma. Using ultradeep sequencing (UDS) data from an intrafamilial case, we detected such mutations at low frequencies among three immunotolerant patients and at high frequencies in an inactive carrier. Furthermore, our analyses indicated that the HBV population from the seroconverter patient underwent many genetic changes in response to virus clearance. Together, these data indicate a potential use of UDS for developing non-invasive biomarkers for monitoring disease changes over time or in response to specific therapies. In addition, our analyses revealed that virus clearance seemed not to require the virus effective population size to decline. A detailed genetic analysis of the viral lineages arising during and after the clearance suggested that mutations at or close to critical elements of the core promoter (enhancer II, epsilon encapsidation signal, TA2, TA3 and direct repeat 1-hormone response element) might be responsible for a sustained replication. This hypothesis requires the decline in virus load to be explained by constant clearance of virus-producing hepatocytes, consistent with the sustained progress towards serious liver conditions experienced by many CHB patients. PMID:26581478

  9. Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers.

    PubMed

    Hodgins, Kathryn A; Yeaman, Sam; Nurkowski, Kristin A; Rieseberg, Loren H; Aitken, Sally N

    2016-06-01

    The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection. Using RNAseq data, we compared gene expression profiles to patterns of divergence and polymorphism in 44 seedlings of lodgepole pine (Pinus contorta) and 39 seedlings of interior spruce (Picea glauca × engelmannii) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress. We found that rapidly diverging genes tend to have greater expression divergence, lower expression levels, reduced levels of synonymous site diversity, and longer proteins than slowly diverging genes. Similar patterns were identified for the untranslated regions, but with some exceptions. We found evidence that genes with low expression levels had a larger fraction of nearly neutral sites, suggesting a primary role for negative selection in determining the association between evolutionary rate and expression level. There was limited evidence for differences in the rate of positive selection among genes with divergent versus conserved expression profiles and some evidence supporting relaxed selection in genes diverging in expression between the species. Finally, we identified a small number of genes that showed evidence of site-specific positive selection using divergence data alone. However, estimates of the proportion of sites fixed by positive selection (α) were in the range of other plant species with large effective population sizes suggesting relatively high rates of adaptive divergence among conifers. PMID:26873578

  10. Plastid sequence evolution: a new pattern of nucleotide substitutions in the Cucurbitaceae.

    PubMed

    Decker-Walters, Deena S; Chung, Sang-Min; Staub, Jack E

    2004-05-01

    Nucleotide substitutions (i.e., point mutations) are the primary driving force in generating DNA variation upon which selection can act. Substitutions called transitions, which entail exchanges between purines (A = adenine, G = guanine) or pyrimidines (C = cytosine, T = thymine), typically outnumber transversions (e.g., exchanges between a purine and a pyrimidine) in a DNA strand. With an increasing number of plant studies revealing a transversion rather than transition bias, we chose to perform a detailed substitution analysis for the plant family Cucurbitaceae using data from several short plastid DNA sequences. We generated a phylogenetic tree for 19 taxa of the tribe Benincaseae and related genera and then scored conservative substitution changes (e.g., those not exhibiting homoplasy or reversals) from the unambiguous branches of the tree. Neither the transition nor (A+T)/(G+C) biases found in previous studies were supported by our overall data. More importantly, we found a novel and symmetrical substitution bias in which Gs had been preferentially replaced by A, As by C, Cs by T, and Ts by G, resulting in the G-->A-->C-->T-->G substitution series. Understanding this pattern will lead to new hypotheses concerning plastid evolution, which in turn will affect the choices of substitution models and other tree-building algorithms for phylogenetic analyses based on nucleotide data.

  11. The Evolution of Main-Sequence and Starburst Galaxies Across Cosmic Time

    NASA Astrophysics Data System (ADS)

    Aravena, Manuel

    2015-08-01

    In the last decade, significant progress has been achieved in the understanding of the evolution of star formation in galaxies as a function of redshift. Its is now clear that the majority of galaxies at z<3 form a nearly linear correlation between their stellar mass and star formation rates and appear to create most of their stars in timescales of ~1 Gyr. At the highest luminosities, a significant fraction of galaxies deviate from this ‘main-sequence’, showing short duty cycles and thus producing most of their stars in a single burst of star formation (‘starburst’) within a few 100 Myr, being likely driven by major merger activity. Despite the large luminosities of starbursts, main-sequence galaxies appear to dominate the star formation density of the Universe at its peak.While progress has been impressive, a number of questions are still unanswered. In this talk, I will review our current observational understanding of this ‘main-sequence’ vs ‘starburst’ galaxy paradigm, and will address how future observations (e.g. with ALMA) will help us to have better insights into the fundamental properties of these galaxies.

  12. Magma evolution in the Ellittico volcano sequence outcropping at Serra Giannicola Grande, Mt. Etna, Italy.

    NASA Astrophysics Data System (ADS)

    Cristofolini, R.; de Rosa, R.; Ferlito, C.; Tripodo, M.

    2003-04-01

    The volcanic sequence examined here outcrops at Serra Giannicola Grande, along the south-western wall of the Valle del Bove (Mt. Etna Volcano), at an elevation between 2230 and 2700 m (Cristofolini et al., 2002). It is referred to the activity of the Ellittico volcanic complex (Ferlito &Cristofolini, 1989), and unconformably lies over on an erosional surface of the Cuvigghiuni synthem (Calvari et al., 1994). Petrological and geochimical investigations on lava flows, showed that: -The analyzed rocks have a Na-alkaline affinity and cover a compositional range from hawaiites to benmoreites and trachytes. -The common mineral association (pl+cpx+ol+mt) of Etnean lavas is present, both as phenocrysts and in groundmass; kaersutite as phenocryst phase isalso present in some of the samples. -The least differentiated lava flows, interbedded with volcanoclastic deposits in the middle part of the sequence, exhibit the widest compositional heterogeneity; they are referable to the existence of distinct magma batches, characterized by differing ascent rates and/or other processes, such as crustal contamination, occurring at shallow levels. It is noteworthy that mafic lavas differ in their contents of K (and Rb) and follow distinct trends of evolution. This suggests that magmas from at least two different sources were feeding the activity of the volcano. -The presence of the most differentiated lavas in the upper part of the sequence, is consistent with the presence of shallow reservoirs during the last stages of the Ellittico activity, where magmas could evolve due to crystal fractionation. The MELTS petrological code (Ghiorso &Sack, 1995) was used in order to quantify the evolution of the different magmas; this program simulates fractionation and assimilation processes in silicate melts under various physical and compositional conditions, and gives as a result compositions of residual liquids and of fractionated solid phases and their amounts. References Calvari, S., Groppelli

  13. A porous proton-relaying metal-organic framework material that accelerates electrochemical hydrogen evolution

    PubMed Central

    Hod, Idan; Deria, Pravas; Bury, Wojciech; Mondloch, Joseph E.; Kung, Chung-Wei; So, Monica; Sampson, Matthew D.; Peters, Aaron W.; Kubiak, Cliff P.; Farha, Omar K.; Hupp, Joseph T.

    2015-01-01

    The availability of efficient hydrogen evolution reaction (HER) catalysts is of high importance for solar fuel technologies aimed at reducing future carbon emissions. Even though Pt electrodes are excellent HER electrocatalysts, commercialization of large-scale hydrogen production technology requires finding an equally efficient, low-cost, earth-abundant alternative. Here, high porosity, metal-organic framework (MOF) films have been used as scaffolds for the deposition of a Ni-S electrocatalyst. Compared with an MOF-free Ni-S, the resulting hybrid materials exhibit significantly enhanced performance for HER from aqueous acid, decreasing the kinetic overpotential by more than 200 mV at a benchmark current density of 10 mA cm−2. Although the initial aim was to improve electrocatalytic activity by greatly boosting the active area of the Ni-S catalyst, the performance enhancements instead were found to arise primarily from the ability of the proton-conductive MOF to favourably modify the immediate chemical environment of the sulfide-based catalyst. PMID:26365764

  14. A porous proton-relaying metal-organic framework material that accelerates electrochemical hydrogen evolution

    SciTech Connect

    Hod, Idan; Deria, Pravas; Bury, Wojciech; Mondloch, Joseph E.; Kung, Chung-Wei; So, Monica; Sampson, Matthew D.; Peters, Aaron W.; Kubiak, Cliff P.; Farha, Omar K.; Hupp, Joseph T.

    2015-09-14

    The availability of efficient hydrogen evolution reaction (HER) catalysts is of high importance for solar fuel technologies aimed at reducing future carbon emissions. Even though Pt electrodes are excellent HER electrocatalysts, commercialization of large-scale hydrogen production technology requires finding an equally efficient, low-cost, earth-abundant alternative. Here, high porosity, metal-organic framework (MOF) films have been used as scaffolds for the deposition of a Ni-S electrocatalyst. Compared with an MOF-free Ni-S, the resulting hybrid materials exhibit significantly enhanced performance for HER from aqueous acid, decreasing the kinetic overpotential by more than 200 mV at a benchmark current density of 10 mA cm−2. In conclusion, although the initial aim was to improve electrocatalytic activity by greatly boosting the active area of the Ni-S catalyst, the performance enhancements instead were found to arise primarily from the ability of the proton-conductive MOF to favourably modify the immediate chemical environment of the sulfide-based catalyst.

  15. Postcopulatory sexual selection is associated with accelerated evolution of sperm morphology.

    PubMed

    Rowe, Melissah; Albrecht, Tomáš; Cramer, Emily R A; Johnsen, Arild; Laskemoen, Terje; Weir, Jason T; Lifjeld, Jan T

    2015-04-01

    Rapid diversification of sexual traits is frequently attributed to sexual selection, though explicit tests of this hypothesis remain limited. Spermatozoa exhibit remarkable variability in size and shape, and studies report a correlation between sperm morphology (sperm length and shape) and sperm competition risk or female reproductive tract morphology. However, whether postcopulatory processes (e.g., sperm competition and cryptic female choice) influence the speed of evolutionary diversification in sperm form is unknown. Using passerine birds, we quantified evolutionary rates of sperm length divergence among lineages (i.e., species pairs) and determined whether these rates varied with the level of sperm competition (estimated as relative testes mass). We found that relative testes mass was significantly and positively associated with more rapid phenotypic divergence in sperm midpiece and flagellum lengths, as well as total sperm length. In contrast, there was no association between relative testes mass and rates of evolutionary divergence in sperm head size, and models suggested that head length is evolutionarily constrained. Our results are the first to show an association between the strength of sperm competition and the speed of sperm evolution, and suggest that postcopulatory sexual selection promotes rapid evolutionary diversification of sperm morphology.

  16. A porous proton-relaying metal-organic framework material that accelerates electrochemical hydrogen evolution

    DOE PAGES

    Hod, Idan; Deria, Pravas; Bury, Wojciech; Mondloch, Joseph E.; Kung, Chung-Wei; So, Monica; Sampson, Matthew D.; Peters, Aaron W.; Kubiak, Cliff P.; Farha, Omar K.; et al

    2015-09-14

    The availability of efficient hydrogen evolution reaction (HER) catalysts is of high importance for solar fuel technologies aimed at reducing future carbon emissions. Even though Pt electrodes are excellent HER electrocatalysts, commercialization of large-scale hydrogen production technology requires finding an equally efficient, low-cost, earth-abundant alternative. Here, high porosity, metal-organic framework (MOF) films have been used as scaffolds for the deposition of a Ni-S electrocatalyst. Compared with an MOF-free Ni-S, the resulting hybrid materials exhibit significantly enhanced performance for HER from aqueous acid, decreasing the kinetic overpotential by more than 200 mV at a benchmark current density of 10 mA cm−2. In conclusion, althoughmore » the initial aim was to improve electrocatalytic activity by greatly boosting the active area of the Ni-S catalyst, the performance enhancements instead were found to arise primarily from the ability of the proton-conductive MOF to favourably modify the immediate chemical environment of the sulfide-based catalyst.« less

  17. Phylogeny and rates of molecular evolution of planktonic foraminifera: SSU rDNA sequences compared to the fossil record.

    PubMed

    de Vargas, C; Zaninetti, L; Hilbrecht, H; Pawlowski, J

    1997-09-01

    Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera. The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently, at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 x 10(-9) substitutions/site/year in the Globigerinidae to less than 1.0 x 10(-9) substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates their effect on phylogenetic reconstructions.

  18. Vulcanian eruptions: experimental insights into leading shock waves, initial acceleration, and flow evolution

    NASA Astrophysics Data System (ADS)

    Clarke, A. B.; Chojnicki, K. N.; Phillips, J. C.

    2008-12-01

    Vulcanian eruptions are frequent, small-scale, short-lived explosions that occur as a result of rapid decompression of a volcanic conduit. Results of two relevant experimental studies are presented here. The first examines the initial burst phase and leading shock waves via 1-D shock-tube experiments in which mixtures of air and spherical particles are rapidly decompressed into a low-pressure environment via diaphragm rupture. Maximum gas-particle mixture velocities decrease with increasing particle diameter for a given initial pressure ratio across the diaphragm. Experiments with particles produce weaker and more slowly propagating shocks relative to experiments with air alone. Comparison of experimental data to theoretical and computational solutions leads to two key results: 1) the effective interphase drag coefficient during high- acceleration stages of an eruption is less than values previously used in multiphase models of explosive eruptions; therefore a new formulation is prescribed; and 2) leading shock waves are formed by the gas phase alone, not the solid-gas mixture, with shock wave characteristics reflecting losses due to drag between air and particles; therefore shock wave calculations should consider these losses rather than treat the system as a perfectly-coupled pseudogas. The second set of experiments examines the subsequent propagation of the pyroclastic jet or plume by injecting discrete pulses of pressurized (negatively or positively) buoyant fluids into fresh water. Dimensional analysis, based on two source parameters, total injected momentum and total injected buoyancy, identifies a universal scaling relationship for the initial propagation of short-duration impulsive flows; the non- dimensional, time-varying velocity varies as the square root of the time-varying, non-dimensional ratio of source parameters. The relationship successfully describes the experimental trends over a wide range of initial conditions as well as flow propagation of

  19. Flow Visualization and Measurements of the Mixing Evolution of a Shock-Accelerated Gas Curtain

    SciTech Connect

    Prestridge, K.; Vorobieff, P.V.; Rightley, P.M.; Benjamin, R.F

    1999-07-19

    We describe a highly-detailed experimental characterization of the impulsively driven Rayleigh-Taylor instability, called the Richtmyer-Meshkov instability. This instability is produced by flowing a diffuse, vertical curtain of heavy gas (SF{sub 6}) into the test section of an air-filled horizontally oriented shock tube. The instability evolves after the passage of a Mach 1.2 shock past the curtain, and the development of the curtain is visualized by seeding the SF{sub 6} with small (d{approximately}0.5 and micro;m) glycol droplets using a modified theatrical fog generator. Because the event lasts only 1 ms and the initial conditions vary from test to test, rapid and complete data acquisition is required in order to characterize the initial and dynamic conditions for each experimental shot. Through the use of a custom-built pulsed Nd: YAG laser, we are able to image the flowfield at seven different times. We acquire a double-pulsed image of the flow with the use of a second pulsed Nd:YAG, which is used to determine the instantaneous velocity field using Particle Image Velocimetry (PIV). During a single experiment, high resolution images of the initial conditions and dynamic conditions are acquired using three CCD cameras. Issues of the fidelity of the flow seeding technique and the reliability of the PIV technique will be addressed. We have successfully provided interesting data through analysis of the images alone, and we are hoping that PIV information will be able to add further physical insight to the evolution of the RM instability and the transition to turbulence.

  20. The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts.

    PubMed

    Wang, Bin; Xue, Jiayu; Li, Libo; Liu, Yang; Qiu, Yin-Long

    2009-12-01

    Plant mitochondrial genomes have been known to be highly unusual in their large sizes, frequent intra-genomic rearrangement, and generally conservative sequence evolution. Recent studies show that in early land plants the mitochondrial genomes exhibit a mixed mode of conservative yet dynamic evolution. Here, we report the completely sequenced mitochondrial genome from the liverwort Pleurozia purpurea. The circular genome has a size of 168,526 base pairs, containing 43 protein-coding genes, 3 rRNA genes, 25 tRNA genes, and 31 group I or II introns. It differs from the Marchantia polymorpha mitochondrial genome, the only other liverwort chondriome that has been sequenced, in lacking two genes (trnRucg and trnTggu) and one intron (rrn18i1065gII). The two genomes have identical gene orders and highly similar sequences in exons, introns, and intergenic spacers. Finally, a comparative analysis of duplicated trnRucu and other trnR genes from the two liverworts and several other organisms identified the recent lateral origin of trnRucg in Marchantia mtDNA through modification of a duplicated trnRucu. This study shows that the mitochondrial genomes evolve extremely slowly in liverworts, the earliest-diverging lineage of extant land plants, in stark contrast to what is known of highly dynamic evolution of mitochondrial genomes in seed plants.

  1. Evolution.

    ERIC Educational Resources Information Center

    Mayr, Ernst

    1978-01-01

    Traces the history of evolution theory from Lamarck and Darwin to the present. Discusses natural selection in detail. Suggests that, besides biological evolution, there is also a cultural evolution which is more rapid than the former. (MA)

  2. Exome sequencing of senescence-accelerated mice (SAM) reveals deleterious mutations in degenerative disease-causing genes

    PubMed Central

    2013-01-01

    Background Senescence-accelerated mice (SAM) are a series of mouse strains originally derived from unexpected crosses between AKR/J and unknown mice, from which phenotypically distinct senescence-prone (SAMP) and -resistant (SAMR) inbred strains were subsequently established. Although SAMP strains have been widely used for aging research focusing on their short life spans and various age-related phenotypes, such as immune dysfunction, osteoporosis, and brain atrophy, the responsible gene mutations have not yet been fully elucidated. Results To identify mutations specific to SAMP strains, we performed whole exome sequencing of 6 SAMP and 3 SAMR strains. This analysis revealed 32,019 to 38,925 single-nucleotide variants in the coding region of each SAM strain. We detected Ogg1 p.R304W and Mbd4 p.D129N deleterious mutations in all 6 of the SAMP strains but not in the SAMR or AKR/J strains. Moreover, we extracted 31 SAMP-specific novel deleterious mutations. In all SAMP strains except SAMP8, we detected a p.R473W missense mutation in the Ldb3 gene, which has been associated with myofibrillar myopathy. In 3 SAMP strains (SAMP3, SAMP10, and SAMP11), we identified a p.R167C missense mutation in the Prx gene, in which mutations causing hereditary motor and sensory neuropathy (Dejerine-Sottas syndrome) have been identified. In SAMP6 we detected a p.S540fs frame-shift mutation in the Il4ra gene, a mutation potentially causative of ulcerative colitis and osteoporosis. Conclusions Our data indicate that different combinations of mutations in disease-causing genes may be responsible for the various phenotypes of SAMP strains. PMID:23586671

  3. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

    PubMed

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z

    2015-01-15

    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

  4. Molecular evolution of viruses of the family Filoviridae based on 97 whole-genome sequences.

    PubMed

    Carroll, Serena A; Towner, Jonathan S; Sealy, Tara K; McMullan, Laura K; Khristova, Marina L; Burt, Felicity J; Swanepoel, Robert; Rollin, Pierre E; Nichol, Stuart T

    2013-03-01

    Viruses in the Ebolavirus and Marburgvirus genera (family Filoviridae) have been associated with large outbreaks of hemorrhagic fever in human and nonhuman primates. The first documented cases occurred in primates over 45 years ago, but the amount of virus genetic diversity detected within bat populations, which have recently been identified as potential reservoir hosts, suggests that the filoviruses are much older. Here, detailed Bayesian coalescent phylogenetic analyses are performed on 97 whole-genome sequences, 55 of which are newly reported, to comprehensively examine molecular evolutionary rates and estimate dates of common ancestry for viruses within the family Filoviridae. Molecular evolutionary rates for viruses belonging to different species range from 0.46 × 10(-4) nucleotide substitutions/site/year for Sudan ebolavirus to 8.21 × 10(-4) nucleotide substitutions/site/year for Reston ebolavirus. Most recent common ancestry can be traced back only within the last 50 years for Reston ebolavirus and Zaire ebolavirus species and suggests that viruses within these species may have undergone recent genetic bottlenecks. Viruses within Marburg marburgvirus and Sudan ebolavirus species can be traced back further and share most recent common ancestors approximately 700 and 850 years before the present, respectively. Examination of the whole family suggests that members of the Filoviridae, including the recently described Lloviu virus, shared a most recent common ancestor approximately 10,000 years ago. These data will be valuable for understanding the evolution of filoviruses in the context of natural history as new reservoir hosts are identified and, further, for determining mechanisms of emergence, pathogenicity, and the ongoing threat to public health.

  5. Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences

    PubMed Central

    Carroll, Serena A.; Towner, Jonathan S.; Sealy, Tara K.; McMullan, Laura K.; Khristova, Marina L.; Burt, Felicity J.; Swanepoel, Robert; Rollin, Pierre E.

    2013-01-01

    Viruses in the Ebolavirus and Marburgvirus genera (family Filoviridae) have been associated with large outbreaks of hemorrhagic fever in human and nonhuman primates. The first documented cases occurred in primates over 45 years ago, but the amount of virus genetic diversity detected within bat populations, which have recently been identified as potential reservoir hosts, suggests that the filoviruses are much older. Here, detailed Bayesian coalescent phylogenetic analyses are performed on 97 whole-genome sequences, 55 of which are newly reported, to comprehensively examine molecular evolutionary rates and estimate dates of common ancestry for viruses within the family Filoviridae. Molecular evolutionary rates for viruses belonging to different species range from 0.46 × 10−4 nucleotide substitutions/site/year for Sudan ebolavirus to 8.21 × 10−4 nucleotide substitutions/site/year for Reston ebolavirus. Most recent common ancestry can be traced back only within the last 50 years for Reston ebolavirus and Zaire ebolavirus species and suggests that viruses within these species may have undergone recent genetic bottlenecks. Viruses within Marburg marburgvirus and Sudan ebolavirus species can be traced back further and share most recent common ancestors approximately 700 and 850 years before the present, respectively. Examination of the whole family suggests that members of the Filoviridae, including the recently described Lloviu virus, shared a most recent common ancestor approximately 10,000 years ago. These data will be valuable for understanding the evolution of filoviruses in the context of natural history as new reservoir hosts are identified and, further, for determining mechanisms of emergence, pathogenicity, and the ongoing threat to public health. PMID:23255795

  6. THE QUADRUPLE PRE-MAIN-SEQUENCE SYSTEM LkCa 3: IMPLICATIONS FOR STELLAR EVOLUTION MODELS

    SciTech Connect

    Torres, Guillermo; Latham, David W.; Ruiz-Rodriguez, Dary; Prato, L.; Wasserman, Lawrence H.; Badenas, Mariona; Schaefer, G. H.; Mathieu, Robert D.

    2013-08-10

    We report the discovery that the pre-main-sequence (PMS) object LkCa 3 in the Taurus-Auriga star-forming region is a hierarchical quadruple system of M stars. It was previously known to be a close ({approx}0.''5) visual pair, with one component being a moderately eccentric 12.94 day single-lined spectroscopic binary. A re-analysis of archival optical spectra complemented by new near-infrared (NIR) spectroscopy shows both visual components to be double lined; the second one has a period of 4.06 days and a circular orbit. In addition to the orbital elements, we determine optical and NIR flux ratios, effective temperatures, and projected rotational velocities for all four stars. Using existing photometric monitoring observations of the system that had previously revealed the rotational period of the primary in the longer-period binary, we also detect the rotational signal of the primary in the 4.06 day binary, which is synchronized with the orbital motion. With only the assumption of coevality, a comparison of all of these constraints with current stellar evolution models from the Dartmouth series points to an age of 1.4 Myr and a distance of 133 pc, consistent with previous estimates for the region and suggesting that the system is on the near side of the Taurus complex. Similar comparisons of the properties of LkCa 3 and the well-known quadruple PMS system GG Tau with the widely used models from the Lyon series for a mixing length parameter of {alpha}{sub ML} = 1.0 strongly favor the Dartmouth models.

  7. Insights into the evolution of vitamin B12 auxotrophy from sequenced algal genomes.

    PubMed

    Helliwell, Katherine E; Wheeler, Glen L; Leptos, Kyriacos C; Goldstein, Raymond E; Smith, Alison G

    2011-10-01

    Vitamin B(12) (cobalamin) is a dietary requirement for humans because it is an essential cofactor for two enzymes, methylmalonyl-CoA mutase and methionine synthase (METH). Land plants and fungi neither synthesize or require cobalamin because they do not contain methylmalonyl-CoA mutase, and have an alternative B(12)-independent methionine synthase (METE). Within the algal kingdom, approximately half of all microalgal species need the vitamin as a growth supplement, but there is no phylogenetic relationship between these species, suggesting that the auxotrophy arose multiple times through evolution. We set out to determine the underlying cellular mechanisms for this observation by investigating elements of B(12) metabolism in the sequenced genomes of 15 different algal species, with representatives of the red, green, and brown algae, diatoms, and coccolithophores, including both macro- and microalgae, and from marine and freshwater environments. From this analysis, together with growth assays, we found a strong correlation between the absence of a functional METE gene and B(12) auxotrophy. The presence of a METE unitary pseudogene in the B(12)-dependent green algae Volvox carteri and Gonium pectorale, relatives of the B(12)-independent Chlamydomonas reinhardtii, suggest that B(12) dependence evolved recently in these lineages. In both C. reinhardtii and the diatom Phaeodactylum tricornutum, growth in the presence of cobalamin leads to repression of METE transcription, providing a mechanism for gene loss. Thus varying environmental conditions are likely to have been the reason for the multiple independent origins of B(12) auxotrophy in these organisms. Because the ultimate source of cobalamin is from prokaryotes, the selective loss of METE in different algal lineages will have had important physiological and ecological consequences for these organisms in terms of their dependence on bacteria. PMID:21551270

  8. Molecular characterization of insulin from squamate reptiles reveals sequence diversity and possible adaptive evolution.

    PubMed

    Yamagishi, Genki; Yoshida, Ayaka; Kobayashi, Aya; Park, Min Kyun

    2016-01-01

    The Squamata are the most adaptive and prosperous group among ectothermic amniotes, reptiles, due to their species-richness and geographically wide habitat. Although the molecular mechanisms underlying their prosperity remain largely unknown, unique features have been reported from hormones that regulate energy metabolism. Insulin, a central anabolic hormone, is one such hormone, as its roles and effectiveness in regulation of blood glucose levels remain to be examined in squamates. In the present study, cDNAs coding for insulin were isolated from multiple species that represent various groups of squamates. The deduced amino acid sequences showed a high degree of divergence, with four lineages showing obviously higher number of amino acid substitutions than most of vertebrates, from teleosts to mammals. Among 18 sites presented to comprise the two receptor binding surfaces (one with 12 sites and the other with 6 sites), substitutions were observed in 13 sites. Among them was the substitution of HisB10, which results in the loss of the ability to hexamerize. Furthermore, three of these substitutions were reported to increase mitogenicity in human analogues. These substitutions were also reported from insulin of hystricomorph rodents and agnathan fishes, whose mitogenic potency have been shown to be increased. The estimated value of the non-synonymous-to-synonymous substitution ratio (ω) for the Squamata clade was larger than those of the other reptiles and aves. Even higher values were estimated for several lineages among squamates. These results, together with the regulatory mechanisms of digestion and nutrient assimilation in squamates, suggested a possible adaptive process through the molecular evolution of squamate INS. Further studies on the roles of insulin, in relation to the physiological and ecological traits of squamate species, will provide an insight into the molecular mechanisms that have led to the adaptivity and prosperity of squamates.

  9. Recent acceleration of ice loss in the Northern Patagonia Icefield based on an updated decennial evolution

    NASA Astrophysics Data System (ADS)

    López, P.; Casassa, G.

    2011-12-01

    Ice elevation changes of the Northern Patagonia Icefield (NPI) were analyzed by comparing three Digital Elevation Models (DEM) corresponding to 1975 (constructed based on topographic maps), the SRTM DEM of 2000 yr and a SPOT 5 DEM of 2005. In addition, the glacier length fluctuations and the surface area evolution between 2001 and 2011 of 25 glaciers of the NPI were studied: the information extracted from the Landsat ETM+ satellite image of 11 March 2001 was compared to the measurements performed based on the Landsat ETM+ satellite image of 19 February 2011. From a global point of view, the majority of the studied glaciers thinned, retreated and lost surface between 2001 and 2011, only few glaciers (Leones, Nef, Pared Sur and Soler) located on the eastern side of the NPI have been stable. Glaciers located on the western side of the NPI suffered a stronger wasting compared to the glaciers located on the eastern side. Overall, over the ablation areas of the NPI (below 1150 m a.s.l.) a more rapid thinning of 2.6 m yr-1 occurred between 2000 and 2005 yr compared to the period 1975-2000, in which a mean thinning of 1.7 m yr-1 was measured for the same zones of the NPI. For the whole period (1975-2005) the most important thinning of the ablation areas has been estimated for HPN-1 Glacier (4.4 m yr-1) followed by Benito (3.4 m yr-1), Fraenkel (2.4 m yr-1), Gualas (2.1 m yr-1) and Acodado glaciers, all of them located on the western side of the NPI. Between 2001 and 2011, a noteworthy retreat of 1.9 km was experienced by Gualas Glacier and by Reichert Glacier with 1.6 km, both located on the north-western side of the NPI. On the south-western side of the NPI, during the same decennia, Steffen Glacier experienced a remarkable retreat of 1.6 km as well. During the 2001-2011 period, Steffen Glacier more than doubled its rate of retreat (compared to the 1979-2001 period) and experienced the disintegration of its main front as well as a lateral tongue that retreated 3.1 km. The

  10. The rbcL gene sequence from chestnut indicates a slow rate of evolution in the Fagaceae.

    PubMed

    Frascaria, N; Maggia, L; Michaud, M; Bousquet, J

    1993-08-01

    The nucleotide sequence was obtained for the chloroplast gene coding for the large subunit of the ribulose 1,5-bisphosphate carboxylase (rbcL) of chestnut (Castanea sativa Mill.), a member of the woody family Fagaceae. Amplification primers downstream and upstream the rbcL open reading frame are also described. By comparing with other angiosperm sequences, we show that the rate of evolution of rbcL in the family Fagaceae is much slower than that observed for the families of annuals analyzed.

  11. The ages of globular cluster stars - Effects of rotation on pre-main-sequence, main-sequence, and turnoff evolution

    NASA Technical Reports Server (NTRS)

    Deliyannis, Constantine P.; Demarque, Pierre; Pinsonneault, Marc H.

    1989-01-01

    Evolutionary sequences for low-metallicity stars (Z ranging from 0.001 to 0.0001) to study the effects of internal stellar rotation on the evolutionary time scales in the pre-main sequence, the main sequence (MS), and around the MS turnoff. Although a substantial amount of angular momentum remains in the interior, rotation is only a minor perturbation on the structure and ages of globular cluster stars. Even models with large initial angular momenta have MS lifetimes that are within 1 percent of those of standard models of the same mass and composition. Therefore, rotation does not affect age estimates of globular clusters from isochrone fitting. Furthermore, the models suggest that because rotation is not likely to affect horizontal-branch (HB) morphology, it does not affect significantly age estimates from the Delta-V method. Nevertheless, the internal angular momentum in the models is consistent with observations of surface rotational velocities on the HB, which require the preservation of a large reservoir of internal angular momentum.

  12. Evolution of the microstructure of unmodified and polymer modified asphalt binders with aging in an accelerated weathering tester.

    PubMed

    Menapace, Ilaria; Masad, Eyad

    2016-09-01

    This paper presents findings on the evolution of the surface microstructure of two asphalt binders, one unmodified and one polymer modified, directly exposed to aging agents with increasing durations. The aging is performed using an accelerated weathering tester, where ultraviolet radiation, oxygen and an increased temperature are applied to the asphalt binder surface. Ultraviolet and dark cycles, which simulated the succession of day and night, alternated during the aging process, and also the temperature varied, which corresponded to typical summer day and night temperatures registered in the state of Qatar. Direct aging of an exposed binder surface is more effective in showing microstructural modifications than previously applied protocols, which involved the heat treatment of binders previously aged with standardized methods. With the new protocol, any molecular rearrangements in the binder surface after aging induced by the heat treatment is prevented. Optical photos show the rippling and degradation of the binder surface due to aging. Microstructure images obtained by means of atomic force microscopy show gradual alteration of the surface due to aging. The original relatively flat microstructure was substituted with a profoundly different microstructure, which significantly protrudes from the surface, and is characterized by various shapes, such as rods, round structures and finally 'flower' or 'leaf' structures. PMID:27059404

  13. Evolution of the microstructure of unmodified and polymer modified asphalt binders with aging in an accelerated weathering tester.

    PubMed

    Menapace, Ilaria; Masad, Eyad

    2016-09-01

    This paper presents findings on the evolution of the surface microstructure of two asphalt binders, one unmodified and one polymer modified, directly exposed to aging agents with increasing durations. The aging is performed using an accelerated weathering tester, where ultraviolet radiation, oxygen and an increased temperature are applied to the asphalt binder surface. Ultraviolet and dark cycles, which simulated the succession of day and night, alternated during the aging process, and also the temperature varied, which corresponded to typical summer day and night temperatures registered in the state of Qatar. Direct aging of an exposed binder surface is more effective in showing microstructural modifications than previously applied protocols, which involved the heat treatment of binders previously aged with standardized methods. With the new protocol, any molecular rearrangements in the binder surface after aging induced by the heat treatment is prevented. Optical photos show the rippling and degradation of the binder surface due to aging. Microstructure images obtained by means of atomic force microscopy show gradual alteration of the surface due to aging. The original relatively flat microstructure was substituted with a profoundly different microstructure, which significantly protrudes from the surface, and is characterized by various shapes, such as rods, round structures and finally 'flower' or 'leaf' structures.

  14. Development of a State Machine Sequencer for the Keck Interferometer: Evolution, Development and Lessons Learned using a CASE Tool Approach

    NASA Technical Reports Server (NTRS)

    Rede, Leonard J.; Booth, Andrew; Hsieh, Jonathon; Summer, Kellee

    2004-01-01

    This paper presents a discussion of the evolution of a sequencer from a simple EPICS (Experimental Physics and Industrial Control System) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a CASE (Computer Aided Software Engineering) tool approach. The main purpose of the sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Hare1 finite state machine, software program designed to orchestrate several lower-level hardware and software hard real time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORB A, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

  15. Development of a state machine sequencer for the Keck Interferometer: evolution, development, and lessons learned using a CASE tool approach

    NASA Astrophysics Data System (ADS)

    Reder, Leonard J.; Booth, Andrew; Hsieh, Jonathan; Summers, Kellee R.

    2004-09-01

    This paper presents a discussion of the evolution of a sequencer from a simple Experimental Physics and Industrial Control System (EPICS) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a Computer Aided Software Engineering (CASE) tool approach. The main purpose of the Interferometer Sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations to be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Harel finite state machine software program designed to orchestrate several lower-level hardware and software hard real-time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORBA, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

  16. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants

    DOE PAGES

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; Giorgi, Elena; Bhattacharya, Tanmoy; Gnanakaran, S.; Lapedes, Alan S.; Learn, Gerald H.; Kreider, Edward F.; Li, Yingying; et al

    2015-10-21

    Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations ofmore » mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.« less

  17. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants

    SciTech Connect

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; Giorgi, Elena; Bhattacharya, Tanmoy; Gnanakaran, S.; Lapedes, Alan S.; Learn, Gerald H.; Kreider, Edward F.; Li, Yingying; Shaw, George M.; Hahn, Beatrice H.; Montefiori, David C.; Alam, S. Munir; Bonsignori, Mattia; Moody, M. Anthony; Liao, Hua-Xin; Gao, Feng; Haynes, Barton

    2015-10-21

    Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations of mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.

  18. Concerted evolution at a multicopy locus in the protozoan parasite Theileria parva: extreme divergence of potential protein-coding sequences.

    PubMed Central

    Bishop, R; Musoke, A; Morzaria, S; Sohanpal, B; Gobright, E

    1997-01-01

    Concerted evolution of multicopy gene families in vertebrates is recognized as an important force in the generation of biological novelty but has not been documented for the multicopy genes of protozoa. A multicopy locus, Tpr, which consists of tandemly arrayed open reading frames (ORFs) containing several repeated elements has been described for Theileria parva. Herein we show that probes derived from the 5'/N-terminal ends of ORFs in the genomic DNAs of T. parva Uganda (1,108 codons) and Boleni (699 codons) hybridized with multicopy sequences in homologous DNA but did not detect similar sequences in the DNA of 14 heterologous T. parva stocks and clones. The probe sequences were, however, protein coding according to predictive algorithms and codon usage. The 3'/C-terminal ends of the Uganda and Boleni ORFs exhibited 75% similarity and identity, respectively, to the previously identified Tpr1 and Tpr2 repetitive elements of T. parva Muguga. Tpr1-homologous sequences were detected in two additional species of Theileria. Eight different Tpr1-homologous transcripts were present in piroplasm mRNA from a single T. parva Muguga-infected animal. The Tpr1 and Tpr2 amino acid sequences contained six predicted membrane-associated segments. The ratio of synonymous to nonsynonymous substitutions indicates that Tpr1 evolves like protein-encoding DNA. The previously determined nucleotide sequence of the gene encoding the p67 antigen is completely identical in T. parva Muguga, Boleni, and Uganda, including the third base in codons. The data suggest that concerted evolution can lead to the radical divergence of coding sequences and that this can be a mechanism for the generation of novel genes. PMID:9032293

  19. Depositional sequence evolution, Paleozoic and early Mesozoic of the central Saharan platform, North Africa

    SciTech Connect

    Sprague, A.R.G. )

    1991-08-01

    Over 30 depositional sequences have been identified in the Paleozoic and lower Mesozoic of the Ghadames basin of eastern Algeria, southern Tunisia, and western Libya. Well logs and lithologic information from more than 500 wells were used to correlate the 30 sequences throughout the basin (total area more than 1 million km{sup 2}). Based on systematic change in the log response of strata in successively younger sequences, five groups of sequences with distinctive characteristics have been identified: Cambro-Ordivician, Upper Silurian-Middle Devonian, Upper Devonian, Carboniferous, and Middle Triassic-Middle Jurassic. Each sequence group is terminated by a major, tectonically enhanced sequence boundary that is immediately overlain (except for the Carboniferous) by a shale-prone interval deposited in response to basin-wide flooding. The four Paleozoic sequence groups were deposited on the Saharan platform, a north facing, clastic-dominated shelf that covered most of North Africa during the Paleozoic. The sequence boundary at the top of the Carboniferous sequence group is one of several Permian-Carboniferous angular unconformities in North Africa related to the Hercynian orogeny. The youngest sequence group (Middle Triassic to Middle Jurassic) is a clastic-evaporite package that onlaps southward onto the top of Paleozoic sequence boundary. The progressive changes from the Cambrian to the Jurassic, in the nature of the Ghadames basin sequences is a reflection of the interplay between basin morphology and tectonics, vegetation, eustasy, climate, and sediment supply.

  20. Distribution and evolution of repeated sequences in genomes of Triatominae (Hemiptera-Reduviidae) inferred from genomic in situ hybridization.

    PubMed

    Pita, Sebastian; Panzera, Francisco; Sánchez, Antonio; Panzera, Yanina; Palomeque, Teresa; Lorite, Pedro

    2014-01-01

    The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily.

  1. Distribution and Evolution of Repeated Sequences in Genomes of Triatominae (Hemiptera-Reduviidae) Inferred from Genomic In Situ Hybridization

    PubMed Central

    Pita, Sebastian; Panzera, Francisco; Sánchez, Antonio; Panzera, Yanina; Palomeque, Teresa; Lorite, Pedro

    2014-01-01

    The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily. PMID:25478792

  2. A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate

    PubMed Central

    Khatri, Bhavin S.; Goldstein, Richard A.

    2015-01-01

    Speciation is fundamental to understanding the huge diversity of life on Earth. Although still controversial, empirical evidence suggests that the rate of speciation is larger for smaller populations. Here, we explore a biophysical model of speciation by developing a simple coarse-grained theory of transcription factor-DNA binding and how their co-evolution in two geographically isolated lineages leads to incompatibilities. To develop a tractable analytical theory, we derive a Smoluchowski equation for the dynamics of binding energy evolution that accounts for the fact that natural selection acts on phenotypes, but variation arises from mutations in sequences; the Smoluchowski equation includes selection due to both gradients in fitness and gradients in sequence entropy, which is the logarithm of the number of sequences that correspond to a particular binding energy. This simple consideration predicts that smaller populations develop incompatibilities more quickly in the weak mutation regime; this trend arises as sequence entropy poises smaller populations closer to incompatible regions of phenotype space. These results suggest a generic coarse-grained approach to evolutionary stochastic dynamics, allowing realistic modelling at the phenotypic level. PMID:25936759

  3. Empirical tests of pre-main-sequence stellar evolution models with eclipsing binaries

    NASA Astrophysics Data System (ADS)

    Stassun, Keivan G.; Feiden, Gregory A.; Torres, Guillermo

    2014-06-01

    We examine the performance of standard pre-main-sequence (PMS) stellar evolution models against the accurately measured properties of a benchmark sample of 26 PMS stars in 13 eclipsing binary (EB) systems having masses 0.04-4.0 M⊙ and nominal ages ≈1-20 Myr. We provide a definitive compilation of all fundamental properties for the EBs, with a careful and consistent reassessment of observational uncertainties. We also provide a definitive compilation of the various PMS model sets, including physical ingredients and limits of applicability. No set of model isochrones is able to successfully reproduce all of the measured properties of all of the EBs. In the H-R diagram, the masses inferred for the individual stars by the models are accurate to better than 10% at ≳1 M⊙, but below 1 M⊙ they are discrepant by 50-100%. Adjusting the observed radii and temperatures using empirical relations for the effects of magnetic activity helps to resolve the discrepancies in a few cases, but fails as a general solution. We find evidence that the failure of the models to match the data is linked to the triples in the EB sample; at least half of the EBs possess tertiary companions. Excluding the triples, the models reproduce the stellar masses to better than ∼10% in the H-R diagram, down to 0.5 M⊙, below which the current sample is fully contaminated by tertiaries. We consider several mechanisms by which a tertiary might cause changes in the EB properties and thus corrupt the agreement with stellar model predictions. We show that the energies of the tertiary orbits are comparable to that needed to potentially explain the scatter in the EB properties through injection of heat, perhaps involving tidal interaction. It seems from the evidence at hand that this mechanism, however it operates in detail, has more influence on the surface properties of the stars than on their internal structure, as the lithium abundances are broadly in good agreement with model predictions. The

  4. Stratigraphic framework and evolution of the Cretaceous continental sequences of the Bauru, Sanfranciscana, and Parecis basins, Brazil

    NASA Astrophysics Data System (ADS)

    Batezelli, Alessandro; Ladeira, Francisco Sergio Bernardes

    2016-01-01

    With the breakup of the supercontinent Gondwana, the South American Plate has undergone an intense process of tectonic restructuring that led to the genesis of the interior basins that encompassed continental sedimentary sequences. The Brazilian Bauru, Sanfranciscana and Parecis basins during Late Cretaceous have had their evolution linked to this process of structuring and therefore have very similar sedimentary characteristics. The purpose of this study is to establish a detailed understanding of alluvial sedimentary processes and architecture within a stratigraphic sequence framework using the concept of the stratigraphic base level or the ratio between the accommodation space and sediment supply. The integration of the stratigraphic and facies data contributed to defining the stratigraphic architecture of the Bauru, Sanfranciscana and Parecis Basins, supporting a model for continental sequences that depicts qualitative changes in the sedimentation rate (S) and accommodation space (A) that occurred during the Cretaceous. This study discusses the origin of the unconformity surfaces (K-0, K-1 and K-1A) that separate Sequences 1, 2A and 2B and the sedimentary characteristics of the Bauru, Sanfranciscana and Parecis Basins from the Aptian to the Maastrichtian, comparing the results with other Cretaceous Brazilian basins. The lower Cretaceous Sequence 1 (Caiuá and Areado groups) is interpreted as a low-accommodation systems tract compound by fluvial and aeolian systems. The upper Cretaceous lacustrine, braided river-dominated alluvial fan and aeolian systems display characteristics of the evolution from high-to low-accommodation systems tracts (Sequences 2A and 2B). Unconformity K-0 is related to the origin of the Bauru Basin itself in the Early Cretaceous. In Sanfranciscana and Parecis basins, the unconformity K-0 marks the contact between aeolian deposits from Lower Cretaceous and Upper Cretaceous alluvial systems (Sequences 1 and 2). Unconformity K-1, which was

  5. Alpine geodynamic evolution of passive and active continental margin sequences in the Tauern Window (eastern Alps, Austria, Italy): a review

    NASA Astrophysics Data System (ADS)

    Kurz, W.; Neubauer, F.; Genser, J.; Dachs, E.

    The Penninic oceanic sequence of the Glockner nappe and the foot-wall Penninic continental margin sequences exposed within the Tauern Window (eastern Alps) have been investigated in detail. Field data as well as structural and petrological data have been combined with data from the literature in order to constrain the geodynamic evolution of these units. Volcanic and sedimentary sequences document the evolution from a stable continent that was formed subsequent to the Variscan orogeny, to its disintegration associated with subsidence and rifting in the Triassic and Jurassic, the formation of the Glockner oceanic basin and its consumption during the Upper Cretaceous and the Paleogene. These units are incorporated into a nappe stack that was formed during the collision between a Penninic Zentralgneis block in the north and a southern Austroalpine block. The Venediger nappe and the Storz nappe are characterized by metamorphic Jurassic shelf deposits (Hochstegen group) and Cretaceous flysch sediments (Kaserer and Murtörl groups), the Eclogite Zone and the Rote Wand-Modereck nappe comprise Permian to Triassic clastic sequences (Wustkogel quartzite) and remnants of platform carbonates (Seidlwinkl group) as well as Jurassic volcanoclastic material and rift sediments (Brennkogel facies), covered by Cretaceous flyschoid sequences. Nappe stacking was contemporaneous to and postdated subduction-related (high-pressure) eclogite and blueschist facies metamorphism. Emplacement of the eclogite-bearing units of the Eclogite zone and the Glockner nappe onto Penninic continental units (Zentralgneis block) occurred subsequent to eclogite facies metamorphism. The Eclogite zone, a former extended continental margin, was subsequently overridden by a pile of basement-cover nappes (Rote Wand-Modereck nappe) along a ductile out-of-sequence thrust. Low-angle normal faults that have developed during the Jurassic extensional phase might have been inverted during nappe emplacement.

  6. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens.

    PubMed

    Shokralla, Shadi; Gibson, Joel F; Nikbakht, Hamid; Janzen, Daniel H; Hallwachs, Winnie; Hajibabaei, Mehrdad

    2014-09-01

    DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content.

  7. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens.

    PubMed

    Shokralla, Shadi; Gibson, Joel F; Nikbakht, Hamid; Janzen, Daniel H; Hallwachs, Winnie; Hajibabaei, Mehrdad

    2014-09-01

    DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content. PMID:24641208

  8. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

    PubMed Central

    Shokralla, Shadi; Gibson, Joel F; Nikbakht, Hamid; Janzen, Daniel H; Hallwachs, Winnie; Hajibabaei, Mehrdad

    2014-01-01

    DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content. PMID:24641208

  9. Evolution of vertebrate IgM: complete amino acid sequence of the constant region of Ambystoma mexicanum mu chain deduced from cDNA sequence.

    PubMed

    Fellah, J S; Wiles, M V; Charlemagne, J; Schwager, J

    1992-10-01

    cDNA clones coding for the constant region of the Mexican axolotl (Ambystoma mexicanum) mu heavy immunoglobulin chain were selected from total spleen RNA, using a cDNA polymerase chain reaction technique. The specific 5'-end primer was an oligonucleotide homologous to the JH segment of Xenopus laevis mu chain. One of the clones, JHA/3, corresponded to the complete constant region of the axolotl mu chain, consisting of a 1362-nucleotide sequence coding for a polypeptide of 454 amino acids followed in 3' direction by a 179-nucleotide untranslated region and a polyA+ tail. The axolotl C mu is divided into four typical domains (C mu 1-C mu 4) and can be aligned with the Xenopus C mu with an overall identity of 56% at the nucleotide level. Percent identities were particularly high between C mu 1 (59%) and C mu 4 (71%). The C-terminal 20-amino acid segment which constitutes the secretory part of the mu chain is strongly homologous to the equivalent sequences of chondrichthyans and of other tetrapods, including a conserved N-linked oligosaccharide, the penultimate cysteine and the C-terminal lysine. The four C mu domains of 13 vertebrate species ranging from chondrichthyans to mammals were aligned and compared at the amino acid level. The significant number of mu-specific residues which are conserved into each of the four C mu domains argues for a continuous line of evolution of the vertebrate mu chain. This notion was confirmed by the ability to reconstitute a consistent vertebrate evolution tree based on the phylogenic parsimony analysis of the C mu 4 sequences. PMID:1382992

  10. A 5.8S nuclear ribosomal RNA gene sequence database: applications to ecology and evolution

    NASA Technical Reports Server (NTRS)

    Cullings, K. W.; Vogler, D. R.

    1998-01-01

    We complied a 5.8S nuclear ribosomal gene sequence database for animals, plants, and fungi using both newly generated and GenBank sequences. We demonstrate the utility of this database as an internal check to determine whether the target organism and not a contaminant has been sequenced, as a diagnostic tool for ecologists and evolutionary biologists to determine the placement of asexual fungi within larger taxonomic groups, and as a tool to help identify fungi that form ectomycorrhizae.

  11. Lithium evolution from Pre-Main Sequence to the Spite plateau: an environmental solution to the cosmological lithium problem

    NASA Astrophysics Data System (ADS)

    Fu, Xiaoting; Bressan, Alessandro; Molaro, Paolo; Marigo, Paola

    2016-08-01

    Lithium abundance derived in metal-poor main sequence stars is about three times lower than the primordial value of the standard Big Bang nucleosynthesis prediction. This disagreement is referred to as the lithium problem. We reconsider the stellar Li evolution from the pre-main sequence to the end of main sequence phase by introducing the effects of overshooting and residual mass accretion. We show that 7Li could be significantly depleted by convective overshooting in the pre-main sequence phase and then partially restored in the stellar atmosphere by residual accretion which follows the Li depletion phase and could be regulated by EUV photo-evaporation. By considering the conventional nuclear burning and diffusion along the main sequence we can reproduce the Spite plateau for stars with initial mass m 0=0.62-0.80 M ⊙, and the Li declining branch for lower mass dwarfs, e.g, m 0=0.57-0.60 M ⊙, for a wide range of metallicities (Z=0.00001 to Z=0.0005), starting from an initial Li abundance A(Li) = 2.72.

  12. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.

    PubMed

    Li, Fuguang; Fan, Guangyi; Lu, Cairui; Xiao, Guanghui; Zou, Changsong; Kohel, Russell J; Ma, Zhiying; Shang, Haihong; Ma, Xiongfeng; Wu, Jianyong; Liang, Xinming; Huang, Gai; Percy, Richard G; Liu, Kun; Yang, Weihua; Chen, Wenbin; Du, Xiongming; Shi, Chengcheng; Yuan, Youlu; Ye, Wuwei; Liu, Xin; Zhang, Xueyan; Liu, Weiqing; Wei, Hengling; Wei, Shoujun; Huang, Guodong; Zhang, Xianlong; Zhu, Shuijin; Zhang, He; Sun, Fengming; Wang, Xingfen; Liang, Jie; Wang, Jiahao; He, Qiang; Huang, Leihuan; Wang, Jun; Cui, Jinjie; Song, Guoli; Wang, Kunbo; Xu, Xun; Yu, John Z; Zhu, Yuxian; Yu, Shuxun

    2015-05-01

    Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.

  13. An ITS phylogeny of Leccinum and an analysis of the evolution of minisatellite-like sequences within ITS1.

    PubMed

    den Bakker, Henk C; Gravendeel, Barbara; Kuyper, Thomas W

    2004-01-01

    Phylogenetic relationships of the European species of Leccinum (Boletales, Boletaceae) were investigated by maximum parsimony, Bayesian and likelihood analyses of nrITS1-5.8S-ITS2 and 28S sequences. The separate gene trees inferred were largely concordant, and their combined analysis indicates that several traditional sectional and species-level taxonomic schemes are artificial. In Leccinum, the nrITS region ranges in size from 694 to 1480 bp. This extreme length heterogeneity is localized to a part of the ITS1 spacer that contains a minisatellite characterized by the repeated presence of CTATTGAAAAG and CTAATAGAAAG core sequences and mutational derivatives thereof. The number of core sequences present in the minisatellite varied from 12 to 36. Intra-individual sequence variation of the minisatellite was always smaller than between different species, indicating that concerted evolution proceeds rapidly enough to retain phylogenetic signal at the infraspecific level. In contrast, the evolutionary pattern exhibited by the major ITS1 repeat types found was homoplastic when mapped onto the species lineages inferred from the combined 5.8S-ITS2 sequences. The minisatellite therefore appears not to be useful for phylogeny reconstruction at or above the species level.

  14. An ITS phylogeny of Leccinum and an analysis of the evolution of minisatellite-like sequences within ITS1.

    PubMed

    den Bakker, Henk C; Gravendeel, Barbara; Kuyper, Thomas W

    2004-01-01

    Phylogenetic relationships of the European species of Leccinum (Boletales, Boletaceae) were investigated by maximum parsimony, Bayesian and likelihood analyses of nrITS1-5.8S-ITS2 and 28S sequences. The separate gene trees inferred were largely concordant, and their combined analysis indicates that several traditional sectional and species-level taxonomic schemes are artificial. In Leccinum, the nrITS region ranges in size from 694 to 1480 bp. This extreme length heterogeneity is localized to a part of the ITS1 spacer that contains a minisatellite characterized by the repeated presence of CTATTGAAAAG and CTAATAGAAAG core sequences and mutational derivatives thereof. The number of core sequences present in the minisatellite varied from 12 to 36. Intra-individual sequence variation of the minisatellite was always smaller than between different species, indicating that concerted evolution proceeds rapidly enough to retain phylogenetic signal at the infraspecific level. In contrast, the evolutionary pattern exhibited by the major ITS1 repeat types found was homoplastic when mapped onto the species lineages inferred from the combined 5.8S-ITS2 sequences. The minisatellite therefore appears not to be useful for phylogeny reconstruction at or above the species level. PMID:21148833

  15. Sequences and evolution of human and squirrel monkey blue opsin genes.

    PubMed

    Shimmin, L C; Mai, P; Li, W H

    1997-04-01

    The sequences of the entire blue opsin gene in the squirrel monkey (Saimiri boliviensis) and the five introns of the human blue opsin gene were obtained. Intron 3 of these genes contains an Alu sequence and intron 4 contains a partial mer13 sequence. A comparison of the squirrel monkey opsin sequence with published mammalian opsin sequences shows that features believed to be functionally critical are all conserved. However, the blue opsin has evolved twice as fast as rhodopsin and is only as conservative as the beta globin, which has evolved at the average rate of mammalian proteins. Interestingly, the interhelical loops are, on average, actually more conservative than the transmembrane alpha helical regions. The introns of the blue opsin gene have evolved at the average rate of introns in primate genes.

  16. Rapid Circumstellar Disk Evolution and an Accelerating Star Formation Rate in the Infrared Dark Cloud M17 SWex

    NASA Astrophysics Data System (ADS)

    Povich, Matthew S.; Townsley, Leisa K.; Robitaille, Thomas P.; Broos, Patrick S.; Orbin, Wesley T.; King, Robert R.; Naylor, Tim; Whitney, Barbara A.

    2016-07-01

    We present a catalog of 840 X-ray sources and first results from a 100 ks Chandra X-ray Observatory imaging study of the filamentary infrared (IR) dark cloud G014.225-00.506, which forms the central regions of a larger cloud complex known as the M17 southwest extension (M17 SWex). In addition to the rich population of protostars and young stellar objects with dusty circumstellar disks revealed by archival data from the Spitzer Space Telescope, we discover a population of X-ray-emitting, intermediate-mass pre-main-sequence stars that lack IR excess emission from circumstellar disks. We model the IR spectral energy distributions of this source population to measure its mass function and place new constraints on the destruction timescales for the inner dust disk for 2-8 M ⊙ stars. We also place a lower limit on the star formation rate (SFR) and find that it is quite high (\\dot{M}≥slant 0.007 M ⊙ yr-1), equivalent to several Orion Nebula Clusters in G14.225-0.506 alone, and likely accelerating. The cloud complex has not produced a population of massive, O-type stars commensurate with its SFR. This absence of very massive (≳20 M ⊙) stars suggests that either (1) M17 SWex is an example of a distributed mode of star formation that will produce a large OB association dominated by intermediate-mass stars but relatively few massive clusters, or (2) the massive cores are still in the process of accreting sufficient mass to form massive clusters hosting O stars.

  17. THE RISE AND FALL OF PASSIVE DISK GALAXIES: MORPHOLOGICAL EVOLUTION ALONG THE RED SEQUENCE REVEALED BY COSMOS

    SciTech Connect

    Bundy, Kevin; Hopkins, Philip; Ma, Chung-Pei; Scarlata, Claudia; Capak, Peter; Carollo, C. M.; Oesch, Pascal; Ellis, Richard S.; Salvato, Mara; Scoville, Nick; Drory, Niv; Leauthaud, Alexie; Koekemoer, Anton M.; Murray, Norman; Ilbert, Olivier; Pozzetti, Lucia

    2010-08-20

    The increasing abundance of passive 'red-sequence' galaxies since z {approx} 1-2 is mirrored by a coincident rise in the number of galaxies with spheroidal morphologies. In this paper, however, we show in detail, that, the correspondence between galaxy morphology and color is not perfect, providing insight into the physical origin of this evolution. Using the COSMOS survey, we study a significant population of red-sequence galaxies with disk-like morphologies. These passive disks typically have Sa-Sb morphological types with large bulges, but they are not confined to dense environments. They represent nearly one-half of all red-sequence galaxies and dominate at lower masses ({approx}<10{sup 10} M{sub sun}) where they are increasingly disk-dominated. As a function of time, the abundance of passive disks with M {sub *} {approx}< 10{sup 11} M{sub sun} increases, but not as fast as red-sequence spheroidals in the same mass range. At higher mass, the passive disk population has declined since z {approx} 1, likely because they transform into spheroidals. Based on these trends, we estimate that as much as 60% of galaxies transitioning onto the red sequence evolve through a passive disk phase. The origin of passive disks therefore has broad implications for our understanding of how star formation shuts down. Because passive disks tend to be more bulge-dominated than their star-forming counterparts, a simple fading of blue disks does not fully explain their origin. We explore the strengths and weaknesses of several more sophisticated explanations, including environmental effects, internal stabilization, and disk regrowth during gas-rich mergers. While previous work has sought to explain color and morphological transformations with a single process, these observations open the way to new insight by highlighting the fact that galaxy evolution may actually proceed through several separate stages.

  18. Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon

    PubMed Central

    Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea

    2016-01-01

    Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on the Direct-Coupling Analysis of the co-evolution between inter-protein residue pairs. We use ribosomal and trp operon proteins as test cases: For the small resp. large ribosomal subunit our approach predicts protein-interaction partners at a true-positive rate of 70% resp. 90% within the first 10 predictions, with areas of 0.69 resp. 0.81 under the ROC curves for all predictions. In the trp operon, it assigns the two largest interaction scores to the only two interactions experimentally known. On the level of residue interactions we show that for both the small and the large ribosomal subunit our approach predicts interacting residues in the system with a true positive rate of 60% and 85% in the first 20 predictions. We use artificial data to show that the performance of our approach depends crucially on the size of the joint multiple sequence alignments and analyze how many sequences would be necessary for a perfect prediction if the sequences were sampled from the same model that we use for prediction. Given the performance of our approach on the test data we speculate that it can be used to detect new interactions, especially in the light of the rapid growth of available sequence data. PMID:26882169

  19. Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon.

    PubMed

    Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea

    2016-01-01

    Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on the Direct-Coupling Analysis of the co-evolution between inter-protein residue pairs. We use ribosomal and trp operon proteins as test cases: For the small resp. large ribosomal subunit our approach predicts protein-interaction partners at a true-positive rate of 70% resp. 90% within the first 10 predictions, with areas of 0.69 resp. 0.81 under the ROC curves for all predictions. In the trp operon, it assigns the two largest interaction scores to the only two interactions experimentally known. On the level of residue interactions we show that for both the small and the large ribosomal subunit our approach predicts interacting residues in the system with a true positive rate of 60% and 85% in the first 20 predictions. We use artificial data to show that the performance of our approach depends crucially on the size of the joint multiple sequence alignments and analyze how many sequences would be necessary for a perfect prediction if the sequences were sampled from the same model that we use for prediction. Given the performance of our approach on the test data we speculate that it can be used to detect new interactions, especially in the light of the rapid growth of available sequence data.

  20. Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon.

    PubMed

    Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea

    2016-01-01

    Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on the Direct-Coupling Analysis of the co-evolution between inter-protein residue pairs. We use ribosomal and trp operon proteins as test cases: For the small resp. large ribosomal subunit our approach predicts protein-interaction partners at a true-positive rate of 70% resp. 90% within the first 10 predictions, with areas of 0.69 resp. 0.81 under the ROC curves for all predictions. In the trp operon, it assigns the two largest interaction scores to the only two interactions experimentally known. On the level of residue interactions we show that for both the small and the large ribosomal subunit our approach predicts interacting residues in the system with a true positive rate of 60% and 85% in the first 20 predictions. We use artificial data to show that the performance of our approach depends crucially on the size of the joint multiple sequence alignments and analyze how many sequences would be necessary for a perfect prediction if the sequences were sampled from the same model that we use for prediction. Given the performance of our approach on the test data we speculate that it can be used to detect new interactions, especially in the light of the rapid growth of available sequence data. PMID:26882169

  1. Evolution of the recombination signal sequences in the Ig heavy-chain variable region locus of mammals

    PubMed Central

    Hassanin, Alexandre; Golub, Rachel; Lewis, Susanna M.; Wu, Gillian E.

    2000-01-01

    The Ig and T cell receptor (TCR) loci have an exceptionally dynamic evolutionary history, but the mechanisms responsible remain a subject of speculation. Ig and TCR genes are unique in vertebrates in that they are assembled from V, D, and J segments by site-specific recombination in developing lymphocytes. Here we examine the extent to which the V(D)J recombination in germline cells may have been responsible for remodeling Ig and TCR loci in mammals by asking whether gene segments have evolved as a unit, or whether, instead, recombination signal sequences (RSSs) and coding sequences have different phylogenies. Four distinct types of RSS have been defined in the human Ig heavy-chain variable region (Vh) locus, namely H1, H2, H3, and H5, and no other RSS type has been detected in other mammalian species. There is a well-supported discrepancy between the evolutionary history of the RSSs as compared with the Vh coding sequences: the RSS type H2 of one Vh gene segment has clearly become replaced by a RSS type H3 during mammalian evolution, between 115 and 65 million years ago. Two general models might explain the RSS swap: the first involves an unequal crossing over, and the second implicates germline activation of V(D)J recombination. The Vh-H2/RSS-H3 recombination product has likely been selected during the evolution of mammals because it provides better V(D)J recombination efficiency. PMID:11027341

  2. Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

    PubMed

    Franks, Steven J; Kane, Nolan C; O'Hara, Niamh B; Tittes, Silas; Rest, Joshua S

    2016-08-01

    There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome-wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late-season drought in California. These ancestor-descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (FST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome-wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution. PMID:27072809

  3. Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic's Era.

    PubMed

    Moroz, Leonid L

    2015-12-01

    The origins of neural systems and centralized brains are one of the major transitions in evolution. These events might occur more than once over 570-600 million years. The convergent evolution of neural circuits is evident from a diversity of unique adaptive strategies implemented by ctenophores, cnidarians, acoels, molluscs, and basal deuterostomes. But, further integration of biodiversity research and neuroscience is required to decipher critical events leading to development of complex integrative and cognitive functions. Here, we outline reference species and interdisciplinary approaches in reconstructing the evolution of nervous systems. In the "omic" era, it is now possible to establish fully functional genomics laboratories aboard of oceanic ships and perform sequencing and real-time analyses of data at any oceanic location (named here as Ship-Seq). In doing so, fragile, rare, cryptic, and planktonic organisms, or even entire marine ecosystems, are becoming accessible directly to experimental and physiological analyses by modern analytical tools. Thus, we are now in a position to take full advantages from countless "experiments" Nature performed for us in the course of 3.5 billion years of biological evolution. Together with progress in computational and comparative genomics, evolutionary neuroscience, proteomic and developmental biology, a new surprising picture is emerging that reveals many ways of how nervous systems evolved. As a result, this symposium provides a unique opportunity to revisit old questions about the origins of biological complexity.

  4. Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

    PubMed

    Franks, Steven J; Kane, Nolan C; O'Hara, Niamh B; Tittes, Silas; Rest, Joshua S

    2016-08-01

    There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome-wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late-season drought in California. These ancestor-descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (FST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome-wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution.

  5. Toward a better knowledge of the molecular evolution of phosphoenolpyruvate carboxylase by comparison of partial cDNA sequences.

    PubMed

    Gehrig, H H; Heute, V; Kluge, M

    1998-01-01

    To get deeper insight into the evolution of phosphoenolpyruvate carboxylase we have identified PEPC fragments (about 1,100 bp) of another 12 plants species not yet investigated in this context. The selected plants include one Chlorophyta, two Bryophyta, four Pteridophyta, and five Spermatophyta species. The obtained phylogenetic trees on PEPC isoforms are the most complete ones up to now available. Independent of their manner of construction, the resulting dendrograms are very similar and fully consistent with the main topology as it is postulated for the evolution of the higher terrestrial plants. We found a distinct clustering of the PEPC sequences of the prokaryotes, the algae, and the spermatophytes. PEPC isoforms of the archegoniates are located in the phylogenetic trees between the algae and spermatophytes. Our results strengthen the view that the PEPC is a very useful molecular marker with which to visualize phylogenetic trends both on the metabolic and organismic levels.

  6. Evolution of the dec-1 eggshell locus in Drosophila. III. Sequence comparisons of the simulans complex repeated domain reveal non-concerted evolution.

    PubMed

    Escher, S A; Lambertsson, A

    1996-01-01

    The X-linked female sterile locus dec-1 (defective chorion-1) was examined in the closely related species D. simulans, D. mauritiana, and D. sechellia (the simulans complex). This locus encodes important eggshell proteins produced in the follicle cells during stages 9 and 12 of oogenesis. In D. melanogaster four variant protein forms have been found, differing in 2-3 kDa each. The variation is due to deletions of 1, 2, or 3 units of a 5-times repeated sequence (78 bp long) of the central coding region. The same type of deletions were found in two variants of D. simulans; in this species, however, the maximum number of repeats observed so far is four. The island species D. mauritiana and D. sechellia both have the repeat sequence repeated three times. Sequence comparisons revealed that the repeats in the simulans complex have been less homogenised by the forces of concerted evolution than the repeats in D. melanogaster. Two domains of the repetitive region that evolve at different rates and are subject to different mechanisms of DNA turnover were also defined.

  7. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

    PubMed Central

    2012-01-01

    The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described. PMID:22293439

  8. Evolution of P transposable elements: sequences of Drosophila nebulosa P elements.

    PubMed Central

    Lansman, R A; Shade, R O; Grigliatti, T A; Brock, H W

    1987-01-01

    P elements have been cloned and sequenced from Drosophila nebulosa. Their sequences have diverged less than 6% from P elements of Drosophila melanogaster. However D. nebulosa P elements have nucleotide changes that close all four open reading frames found in the D. melanogaster P element. Microinjection experiments show that D. nebulosa P elements cannot provide transposase function for D. melanogaster P elements, nor are D. nebulosa P elements mobilized by the transposase provided by a D. melanogaster P factor. Three D. nebulosa P elements appear to have integrated into the same position of a complex, centromeric repeated sequence. Comparison of nucleotide sequences suggests that D. nebulosa P elements have diverged upon different pathways from a common ancestor that was 99% homologous to the P elements of D. melanogaster. PMID:2819880

  9. Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131.

    PubMed

    Johnson, Timothy J; Danzeisen, Jessica L; Youmans, Bonnie; Case, Kyle; Llop, Katharine; Munoz-Aguayo, Jeannette; Flores-Figueroa, Cristian; Aziz, Maliha; Stoesser, Nicole; Sokurenko, Evgeni; Price, Lance B; Johnson, James R

    2016-01-01

    The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with the H30R/C1 clade, whereas an F2:A1:B- plasmid is associated with the H30Rx/C2 clade. A series of plasmid gene losses, gains, and rearrangements involving IS26 likely led to the current plasmid complements within each ST131-H30 sublineage, which contain several overlapping gene clusters with putative functions in virulence and fitness, suggesting plasmid-mediated convergent evolution. Evidence suggests that the H30Rx/C2-associated F2:A1:B- plasmid type was present in strains ancestral to the acquisition of fluoroquinolone resistance and prior to the introduction of a multidrug resistance-encoding gene cassette harboring bla CTX-M-15. In vitro experiments indicated a host strain-independent low frequency of plasmid transfer, differential levels of plasmid stability even between closely related ST131-H30 strains, and possible epistasis for carriage of these plasmids within the H30R/Rx lineages. IMPORTANCE A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131's evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST

  10. Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131

    PubMed Central

    Danzeisen, Jessica L.; Youmans, Bonnie; Case, Kyle; Llop, Katharine; Munoz-Aguayo, Jeannette; Flores-Figueroa, Cristian; Aziz, Maliha; Sokurenko, Evgeni; Price, Lance B.; Johnson, James R.

    2016-01-01

    ABSTRACT The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with the H30R/C1 clade, whereas an F2:A1:B− plasmid is associated with the H30Rx/C2 clade. A series of plasmid gene losses, gains, and rearrangements involving IS26 likely led to the current plasmid complements within each ST131-H30 sublineage, which contain several overlapping gene clusters with putative functions in virulence and fitness, suggesting plasmid-mediated convergent evolution. Evidence suggests that the H30Rx/C2-associated F2:A1:B− plasmid type was present in strains ancestral to the acquisition of fluoroquinolone resistance and prior to the introduction of a multidrug resistance-encoding gene cassette harboring blaCTX-M-15. In vitro experiments indicated a host strain-independent low frequency of plasmid transfer, differential levels of plasmid stability even between closely related ST131-H30 strains, and possible epistasis for carriage of these plasmids within the H30R/Rx lineages. IMPORTANCE A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical

  11. Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131.

    PubMed

    Johnson, Timothy J; Danzeisen, Jessica L; Youmans, Bonnie; Case, Kyle; Llop, Katharine; Munoz-Aguayo, Jeannette; Flores-Figueroa, Cristian; Aziz, Maliha; Stoesser, Nicole; Sokurenko, Evgeni; Price, Lance B; Johnson, James R

    2016-01-01

    The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with the H30R/C1 clade, whereas an F2:A1:B- plasmid is associated with the H30Rx/C2 clade. A series of plasmid gene losses, gains, and rearrangements involving IS26 likely led to the current plasmid complements within each ST131-H30 sublineage, which contain several overlapping gene clusters with putative functions in virulence and fitness, suggesting plasmid-mediated convergent evolution. Evidence suggests that the H30Rx/C2-associated F2:A1:B- plasmid type was present in strains ancestral to the acquisition of fluoroquinolone resistance and prior to the introduction of a multidrug resistance-encoding gene cassette harboring bla CTX-M-15. In vitro experiments indicated a host strain-independent low frequency of plasmid transfer, differential levels of plasmid stability even between closely related ST131-H30 strains, and possible epistasis for carriage of these plasmids within the H30R/Rx lineages. IMPORTANCE A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131's evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST

  12. Accelerated Cardiac T2 Mapping using Breath-hold Multi-Echo Fast Spin-Echo Pulse Sequence with Compressed sensing and Parallel Imaging

    PubMed Central

    Feng, Li; Otazo, Ricardo; Jung, Hong; Jensen, Jens H.; Ye, Jong C.; Sodickson, Daniel K.; Kim, Daniel

    2010-01-01

    Cardiac T2 mapping is a promising method for quantitative assessment of myocardial edema and iron overload. We have developed a new multi-echo fast spin echo (ME-FSE) pulse sequence for breath-hold T2 mapping with acceptable spatial resolution. We propose to further accelerate this new ME-FSE pulse sequence using k-t FOCal Underdetermined System Solver (FOCUSS) adapted with a framework that utilizes both compressed sensing and parallel imaging (.e.g, GRAPPA) to achieve higher spatial resolution. We imaged twelve control subjects in mid-ventricular short-axis planes and compared the accuracy of T2 measurements obtained using ME-FSE with GRAPPA and ME-FSE with k-t FOCUSS. For image reconstruction, we used a bootstrapping two-step approach, where in the first step fast Fourier transform was used as the sparsifying transform and in the final step principal component analysis was used as the sparsifying transform. Compared with T2 measurements obtained using GRAPPA, T2 measurements obtained using k-t FOCUSS were in excellent agreement (mean difference = 0.04 ms; upper/lower 95% limits of agreement were 2.26/−2.19 ms). The proposed accelerated ME-FSE pulse sequence with k-t FOCUSS is a promising investigational method for rapid T2 measurement of the heart with relatively high spatial resolution (1.7 mm × 1.7 mm). PMID:21360737

  13. Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family.

    PubMed

    Li, Gang; Janecka, Jan E; Murphy, William J

    2011-02-01

    Cauxin is a novel urinary protein recently identified in the domestic cat that regulates the excretion of felinine, a pheromone precursor involved in sociochemical communication and territorial marking of domestic and wild felids. Understanding the evolutionary history of cauxin may therefore illuminate molecular adaptations involved in the evolution of pheromone-based communication, recognition, and mate selection in wild animals. We sequenced the gene encoding cauxin, CES7, in 22 species representing all major felid lineages, and multiple outgroups and showed that it has undergone rapid evolutionary change preceding and during the diversification of the cat family. A comparison between feline cauxin and orthologous carboxylesterases from other mammalian lineages revealed evidence of strong positive Darwinian selection within and between several cat lineages, enriched at functionally important sites of the protein. The higher rate of radical amino acid replacements in small felids, coupled with the lack of felinine and extremely low levels of cauxin in the urine of the great cats (Panthera), correlates with functional divergence of this gene in Panthera, and its putative loss in the snow leopard. Expression studies found evidence for several alternatively spliced transcripts in testis and brain, suggesting additional roles in male reproductive fitness and behavior. Our work presents the first report of strong positive natural selection acting on a major urinary protein of nonrodent mammals, providing evidence for parallel selection pressure on the regulation of pheromones in different mammalian lineages, despite the use of different metabolic pathways. Our results imply that natural selection may drive rapid changes in the regulation of pheromones in urine among the different cat species, which in turn may influence social behavior, such as territorial marking and conspecific recognition, therefore serving as an important mechanism for the radiation of this group

  14. Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family.

    PubMed

    Li, Gang; Janecka, Jan E; Murphy, William J

    2011-02-01

    Cauxin is a novel urinary protein recently identified in the domestic cat that regulates the excretion of felinine, a pheromone precursor involved in sociochemical communication and territorial marking of domestic and wild felids. Understanding the evolutionary history of cauxin may therefore illuminate molecular adaptations involved in the evolution of pheromone-based communication, recognition, and mate selection in wild animals. We sequenced the gene encoding cauxin, CES7, in 22 species representing all major felid lineages, and multiple outgroups and showed that it has undergone rapid evolutionary change preceding and during the diversification of the cat family. A comparison between feline cauxin and orthologous carboxylesterases from other mammalian lineages revealed evidence of strong positive Darwinian selection within and between several cat lineages, enriched at functionally important sites of the protein. The higher rate of radical amino acid replacements in small felids, coupled with the lack of felinine and extremely low levels of cauxin in the urine of the great cats (Panthera), correlates with functional divergence of this gene in Panthera, and its putative loss in the snow leopard. Expression studies found evidence for several alternatively spliced transcripts in testis and brain, suggesting additional roles in male reproductive fitness and behavior. Our work presents the first report of strong positive natural selection acting on a major urinary protein of nonrodent mammals, providing evidence for parallel selection pressure on the regulation of pheromones in different mammalian lineages, despite the use of different metabolic pathways. Our results imply that natural selection may drive rapid changes in the regulation of pheromones in urine among the different cat species, which in turn may influence social behavior, such as territorial marking and conspecific recognition, therefore serving as an important mechanism for the radiation of this group

  15. Cretaceous sequence stratigraphy of the Northern South American Passive Margin: Implications for tectonic evolution

    SciTech Connect

    Kauffman, E.G.; Villamil, T.; Johnson, C.C. )

    1993-02-01

    The passive margin of northern South America, from Colombia to northeastern Venezuela, was relatively stable through the Cretaceous and only broadly affected by the entry of the Caribbean Plate into the Protocaribbean Basin. This region offers a unique opportunity to test the relative effects of global sealevel change, autocyclic sedimentologic processed, and regional tectonics in shaping the stratigraphic record of Cretaceous passive margins. High-resolution stratigraphic studies of Colombia and Venezuela have established a precise system of regional chronology and correlation with resolution <1 Ma (50-500 ka for the middle Cretaceous). This allows precise separation of allocyclic and autocyclic controls on facies development. This new chronology integrates assemblage zone biostratigraphy with event/cycle chronostratigraphy. Newly measured Cretaceous sections in Venezuela and throughout Colombia are calibrated to this new chronology, and sequence stratigraphic units independently defined to the third-order of resolution. Graphic correlation of all sections is used to identify sequences with regional stratigraphic expression, and those which correlate to sequence stratigraphic standards of North America, Europe and the global cycles of Hag et al. (1988). 50-60 percent of the stratigraphic sequences across the South American passive margin correlate to other continents and to the global sequence stratigraphic standard, reflecting strong eustatic influence on Cretaceous sedimentation across northern South America. The remaining sequences in this region reflect tectonic modification of the passive margin and autocyclic sedimentary processes.

  16. The preference of the mitochondrial endonuclease for a conserved sequence block in mitochondrial DNA is highly conserved during mammalian evolution.

    PubMed Central

    Low, R L; Buzan, J M; Couper, C L

    1988-01-01

    Endonuclease activity identified in crude preparations of rat and human heart mitochondria has each been partially purified and characterized. Both the rat and human activities purify as a single enzyme that closely resembles the endonuclease of bovine-heart mitochondria (Cummings, O.W. et. al. (1987) J. Biol. Chem. 262:2005-2015). All three enzymes, for example elute similarly during gel filtration and DNA-cellulose chromatography, and exhibit similar enzymatic properties. Although the nucleotide sequences of the mtDNAs indicate that there has occurred an unusual degree of divergence in the displacement-loop region during mammalian evolution, the nucleotide specificities of the mt endonucleases appear highly conserved and show a striking preference for an evolutionarily-conserved sequence tract that is located upstream from the heavy (H)-strand origin of DNA replication (OriH). Images PMID:3399407

  17. Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family

    SciTech Connect

    Sharrock, R.A.; Quail, P.H. )

    1989-01-01

    Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. The authors have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that they have low sequence identity with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far red light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.

  18. Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia.

    PubMed

    Salvi, Daniele; Mariottini, Paolo

    2012-11-01

    In this study, we analyzed the nuclear ITS2 rRNA primary sequence and secondary structure in Veneridae and comparatively with 20 Bivalvia taxa to test the phylogenetic resolution of this marker and its suitability for molecular diagnosis at different taxonomic levels. Maximum likelihood and Bayesian trees based on primary sequences were congruent with (profile-) neighbor-joining trees based on a combined model of sequence-structure evolution. ITS2 showed higher resolution below the subfamily level, providing a phylogenetic signal comparable to (mitochondrial/nuclear) gene fragments 2-5 times longer. Structural elements of the ITS2 folding, such as specific mismatch pairing and compensatory base changes, provided further support for the monophyly of some groups and for their phylogenetic relationships. Veneridae ITS2 folding is structured in six domains (DI-VI) and shows five striking sequence-structure features. Two of them, the Basal and Apical STEMs, are common to Bivalvia, while the presence of both the Branched STEM and the Y/R stretches occurs in five superfamilies of the two Heterodonta orders Myoida and Veneroida, thus questioning their reciprocal monophyly. Our results validated the ITS2 as a suitable marker for venerids phylogenetics and taxonomy, and underlined the significance of including secondary structure information for both applications at several systematic levels within bivalves.

  19. Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny.

    PubMed

    Raincrow, Jeremy D; Dewar, Ken; Stocsits, Claudia; Prohaska, Sonja J; Amemiya, Chris T; Stadler, Peter F; Chiu, Chi-Hua

    2011-09-15

    Teleost fishes have extra Hox gene clusters owing to shared or lineage-specific genome duplication events in rayfinned fish (actinopterygian) phylogeny. Hence, extrapolating between genome function of teleosts and human or even between different fish species is difficult. We have sequenced and analyzed Hox gene clusters of the Senegal bichir (Polypterus senegalus), an extant representative of the most basal actinopterygian lineage. Bichir possesses four Hox gene clusters (A, B, C, D); phylogenetic analysis supports their orthology to the four Hox gene clusters of the gnathostome ancestor. We have generated a comprehensive database of conserved Hox noncoding sequences that include cartilaginous, lobe-finned, and ray-finned fishes (bichir and teleosts). Our analysis identified putative and known Hox cis-regulatory sequences with differing depths of conservation in Gnathostoma. We found that although bichir possesses four Hox gene clusters, its pattern of conservation of noncoding sequences is mosaic between outgroups, such as human, coelacanth, and shark, with four Hox gene clusters and teleosts, such as zebrafish and pufferfish, with seven or eight Hox gene clusters. Notably, bichir Hox gene clusters have been invaded by DNA transposons and this trend is further exemplified in teleosts, suggesting an as yet unrecognized mechanism of genome evolution that may explain Hox cluster plasticity in actinopterygians. Taken together, our results suggest that actinopterygian Hox gene clusters experienced a reduction in selective constraints that surprisingly predates the teleost-specific genome duplication.

  20. Evolution of tissue-specific keratins as deduced from novel cDNA sequences of the lungfish Protopterus aethiopicus.

    PubMed

    Schaffeld, Michael; Bremer, Miriam; Hunzinger, Christian; Markl, Jürgen

    2005-03-01

    Lungfishes are possibly the closest extant relatives of the land vertebrates (tetrapods). We report here the cDNA and predicted amino acid sequences of 13 different keratins (ten type I and three type II) of the lungfish Protopterus aethiopicus. These keratins include the orthologs of human K8 and K18. The lungfish keratins were also identified in tissue extracts using two-dimensional polyacrylamide gel electrophoresis, keratin blot binding assays and immunoblotting. The identified keratin spots were analyzed by peptide mass fingerprinting which assigned seven sequences (inclusively Protopterus K8 and K18) to their respective protein spot. The peptide mass fingerprints also revealed the fact that the major epidermal type I and type II keratins of this lungfish have not yet been sequenced. Nevertheless, phylogenetic trees constructed from multiple sequence alignments of keratins from lungfish and distantly related vertebrates such as lamprey, shark, trout, frog, and human reveal new insights into the evolution of K8 and K18, and unravel a variety of independent keratin radiation events. PMID:15819414

  1. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

    PubMed

    Thomas, Paul D; Kejariwal, Anish; Guo, Nan; Mi, Huaiyu; Campbell, Michael J; Muruganujan, Anushya; Lazareva-Ulitsky, Betty

    2006-07-01

    The vast amount of protein sequence data now available, together with accumulating experimental knowledge of protein function, enables modeling of protein sequence and function evolution. The PANTHER database was designed to model evolutionary sequence-function relationships on a large scale. There are a number of applications for these data, and we have implemented web services that address three of them. The first is a protein classification service. Proteins can be classified, using only their amino acid sequences, to evolutionary groups at both the family and subfamily levels. Specific subfamilies, and often families, are further classified when possible according to their functions, including molecular function and the biological processes and pathways they participate in. The second application, then, is an expression data analysis service, where functional classification information can help find biological patterns in the data obtained from genome-wide experiments. The third application is a coding single-nucleotide polymorphism scoring service. In this case, information about evolutionarily related proteins is used to assess the likelihood of a deleterious effect on protein function arising from a single substitution at a specific amino acid position in the protein. All three web services are available at http://www.pantherdb.org/tools.

  2. Sequence of Stages in the Microstructure Evolution in Copper under Mild Reciprocating Tribological Loading.

    PubMed

    Greiner, Christian; Liu, Zhilong; Strassberger, Luis; Gumbsch, Peter

    2016-06-22

    Tailoring the surface properties of a material for low friction and little wear has long been a goal of tribological research. Since the microstructure of the material under the contact strongly influences tribological performance, the ability to control this microstructure is thereby of key importance. However, there is a significant lack of knowledge about the elementary mechanisms of microstructure evolution under tribological load. To cover different stages of this microstructure evolution, high-purity copper was investigated after increasing numbers of sliding cycles of a sapphire sphere in reciprocating motion. Scanning electron and focused ion beam (FIB) microscopy were applied to monitor the microstructure changes. A thin tribologically deformed layer which grew from tens of nanometers to several micrometers with increasing number of cycles was observed in cross-sections. By analyzing dislocation structures and local orientation changes in the cross-sectional areas, dislocation activity, the occurrence of a distinct dislocation trace line, and the emergence of new subgrain boundaries could be observed at different depths. These results strongly suggest that dislocation self-organization is a key elementary mechanism for the microstructure evolution under a tribological load. The distinct elementary processes at different stages of sliding identified here will be essential for the future modeling of the microstructure evolution in tribological contacts.

  3. Evolution and homologous recombination of the hemagglutinin-esterase gene sequences from porcine torovirus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of the present study was to gain new insights into the evolution, homologous recombination and selection pressures imposed on the porcine torovirus (PToV), by examining changes in the hemagglutinin-esterase (HE) gene. The most recent common ancestor of PToV was estimated to have emerge...

  4. Sequence of Stages in the Microstructure Evolution in Copper under Mild Reciprocating Tribological Loading.

    PubMed

    Greiner, Christian; Liu, Zhilong; Strassberger, Luis; Gumbsch, Peter

    2016-06-22

    Tailoring the surface properties of a material for low friction and little wear has long been a goal of tribological research. Since the microstructure of the material under the contact strongly influences tribological performance, the ability to control this microstructure is thereby of key importance. However, there is a significant lack of knowledge about the elementary mechanisms of microstructure evolution under tribological load. To cover different stages of this microstructure evolution, high-purity copper was investigated after increasing numbers of sliding cycles of a sapphire sphere in reciprocating motion. Scanning electron and focused ion beam (FIB) microscopy were applied to monitor the microstructure changes. A thin tribologically deformed layer which grew from tens of nanometers to several micrometers with increasing number of cycles was observed in cross-sections. By analyzing dislocation structures and local orientation changes in the cross-sectional areas, dislocation activity, the occurrence of a distinct dislocation trace line, and the emergence of new subgrain boundaries could be observed at different depths. These results strongly suggest that dislocation self-organization is a key elementary mechanism for the microstructure evolution under a tribological load. The distinct elementary processes at different stages of sliding identified here will be essential for the future modeling of the microstructure evolution in tribological contacts. PMID:27246396

  5. Nucleotide sequences of immunoglobulin eta genes of chimpanzee and orangutan: DNA molecular clock and hominoid evolution

    SciTech Connect

    Sakoyama, Y.; Hong, K.J.; Byun, S.M.; Hisajima, H.; Ueda, S.; Yaoita, Y.; Hayashida, H.; Miyata, T.; Honjo, T.

    1987-02-01

    To determine the phylogenetic relationships among hominoids and the dates of their divergence, the complete nucleotide sequences of the constant region of the immunoglobulin eta-chain (C/sub eta1/) genes from chimpanzee and orangutan have been determined. These sequences were compared with the human eta-chain constant-region sequence. A molecular clock (silent molecular clock), measured by the degree of sequence divergence at the synonymous (silent) positions of protein-encoding regions, was introduced for the present study. From the comparison of nucleotide sequences of ..cap alpha../sub 1/-antitrypsin and ..beta..- and delta-globulin genes between humans and Old World monkeys, the silent molecular clock was calibrated: the mean evolutionary rate of silent substitution was determined to be 1.56 x 10/sup -9/ substitutions per site per year. Using the silent molecular clock, the mean divergence dates of chimpanzee and orangutan from the human lineage were estimated as 6.4 +/- 2.6 million years and 17.3 +/- 4.5 million years, respectively. It was also shown that the evolutionary rate of primate genes is considerably slower than those of other mammalian genes.

  6. A decade of pig genome sequencing: a window on pig domestication and evolution.

    PubMed

    Groenen, Martien A M

    2016-03-29

    Insight into how genomes change and adapt due to selection addresses key questions in evolutionary biology and in domestication of animals and plants by humans. In that regard, the pig and its close relatives found in Africa and Eurasia represent an excellent group of species that enables studies of the effect of both natural and human-mediated selection on the genome. The recent completion of the draft genome sequence of a domestic pig and the development of next-generation sequencing technology during the past decade have created unprecedented possibilities to address these questions in great detail. In this paper, I review recent whole-genome sequencing studies in the pig and closely-related species that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals.

  7. Analyzing radial acceleration with a smartphone acceleration sensor

    NASA Astrophysics Data System (ADS)

    Vogt, Patrik; Kuhn, Jochen

    2013-03-01

    This paper continues the sequence of experiments using the acceleration sensor of smartphones (for description of the function and the use of the acceleration sensor, see Ref. 1) within this column, in this case for analyzing the radial acceleration.

  8. Large Scale Sequencing of Dothideomycetes Provides Insights into Genome Evolution and Adaptation

    SciTech Connect

    Haridas, Sajeet; Crous, Pedro; Binder, Manfred; Spatafora, Joseph; Grigoriev, Igor

    2015-03-16

    Dothideomycetes is the largest and most diverse class of ascomycete fungi with 23 orders 110 families, 1300 genera and over 19,000 known species. We present comparative analysis of 70 Dothideomycete genomes including over 50 that we sequenced and are as yet unpublished. This extensive sampling has almost quadrupled the previous study of 18 species and uncovered a 10 fold range of genome sizes. We were able to clarify the phylogenetic positions of several species whose origins were unclear in previous morphological and sequence comparison studies. We analyzed selected gene families including proteases, transporters and small secreted proteins and show that major differences in gene content is influenced by speciation.

  9. Epoch-based likelihood models reveal no evidence for accelerated evolution of viviparity in squamate reptiles in response to cenozoic climate change.

    PubMed

    King, Benedict; Lee, Michael S Y

    2015-09-01

    A broad scale analysis of the evolution of viviparity across nearly 4,000 species of squamates revealed that origins increase in frequency toward the present, raising the question of whether rates of change have accelerated. We here use simulations to show that the increased frequency is within the range expected given that the number of squamate lineages also increases with time. Novel, epoch-based methods implemented in BEAST (which allow rates of discrete character evolution to vary across time-slices) also give congruent results, with recent epochs having very similar rates to older epochs. Thus, contrary to expectations, there was no accelerated burst of origins of viviparity in response to global cooling during the Cenozoic or glacial cycles during the Plio-Pleistocene. However, if one accepts the conventional view that viviparity is more likely to evolve than to be lost, and also the evidence here that viviparity has evolved with similar regularity throughout the last 200 Ma, then the absence of large, ancient clades of viviparous squamates (analogs to therian mammals) requires explanation. Viviparous squamate lineages might be more prone to extinction than are oviparous lineages, due to their prevalance at high elevations and latitudes and thus greater susceptibility to climate fluctuations. If so, the directional bias in character evolution would be offset by the bias in extinction rates.

  10. Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (Deleted in AZoospermia) genes.

    PubMed

    Hughes, Jennifer F; Skaletsky, Helen; Page, David C

    2012-12-01

    Studies of Y chromosome evolution often emphasize gene loss, but this loss has been counterbalanced by addition of new genes. The DAZ genes, which are critical to human spermatogenesis, were acquired by the Y chromosome in the ancestor of Old World monkeys and apes. We and our colleagues recently sequenced the rhesus macaque Y chromosome, and comparison of this sequence to human and chimpanzee enables us to reconstruct much of the evolutionary history of DAZ. We report that DAZ arrived on the Y chromosome about 38 million years ago via the transposition of at least 1.1 megabases of autosomal DNA. This transposition also brought five additional genes to the Y chromosome, but all five genes were subsequently lost through mutation or deletion. As the only surviving gene, DAZ experienced extensive restructuring, including intragenic amplification and gene duplication, and has been the target of positive selection in the chimpanzee lineage. Editor's suggested further reading in BioEssays Should Y stay or should Y go: The evolution of non-recombining sex chromosomes Abstract. PMID:23055411

  11. Clonal Evolution Revealed by Whole Genome Sequencing in a Case of Primary Myelofibrosis Transformed to Secondary Acute Myeloid Leukemia

    PubMed Central

    Engle, Elizabeth K.; Fisher, Daniel A.C.; Miller, Christopher A.; McLellan, Michael D.; Fulton, Robert S.; Moore, Deborah M.; Wilson, Richard K.; Ley, Timothy J.; Oh, Stephen T.

    2014-01-01

    Clonal architecture in myeloproliferative neoplasms (MPNs) is poorly understood. Here we report genomic analyses of a patient with primary myelofibrosis (PMF) transformed to secondary acute myeloid leukemia (sAML). Whole genome sequencing (WGS) was performed on PMF and sAML diagnosis samples, with skin included as a germline surrogate. Deep sequencing validation was performed on the WGS samples and an additional sample obtained during sAML remission/relapsed PMF. Clustering analysis of 649 validated somatic single nucleotide variants revealed four distinct clonal groups, each including putative driver mutations. The first group (including JAK2 and U2AF1), representing the founding clone, included mutations with high frequency at all three disease stages. The second clonal group (including MYB) was present only in PMF, suggesting the presence of a clone that was dispensable for transformation. The third group (including ASXL1) contained mutations with low frequency in PMF and high frequency in subsequent samples, indicating evolution of the dominant clone with disease progression. The fourth clonal group (including IDH1 and RUNX1) was acquired at sAML transformation and was predominantly absent at sAML remission/relapsed PMF. Taken together, these findings illustrate the complex clonal dynamics associated with disease evolution in MPNs and sAML. PMID:25252869

  12. The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution.

    PubMed

    Cao, Hieu Xuan; Vu, Giang Thi Ha; Wang, Wenqin; Appenroth, Klaus J; Messing, Joachim; Schubert, Ingo

    2016-01-01

    Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. We selected physically mapped bacterial artificial chromosomes (BACs) containing Spirodela DNA inserts with little or no repetitive elements as probes for multicolor fluorescence in situ hybridization (mcFISH), using an optimized BAC pooling strategy, to validate its physical map and correlate it with its chromosome complement. By consecutive mcFISH analyses, we assigned the originally assembled 32 pseudomolecules (supercontigs) of the genomic sequences to the 20 chromosomes of S. polyrhiza. A Spirodela cytogenetic map containing 96 BAC markers with an average distance of 0.89 Mbp was constructed. Using a cocktail of 41 BACs in three colors, all chromosome pairs could be individualized simultaneously. Seven ancestral blocks emerged from duplicated chromosome segments of 19 Spirodela chromosomes. The chromosomally integrated genome of S. polyrhiza and the established prerequisites for comparative chromosome painting enable future studies on the chromosome homoeology and karyotype evolution of duckweed species.

  13. Molecular evolution and diversity of Conus peptide toxins, as revealed by gene structure and intron sequence analyses.

    PubMed

    Wu, Yun; Wang, Lei; Zhou, Maojun; You, Yuwen; Zhu, Xiaoyan; Qiang, Yuanyuan; Qin, Mengying; Luo, Shaonan; Ren, Zhenghua; Xu, Anlong

    2013-01-01

    Cone snails, which are predatory marine gastropods, produce a cocktail of venoms used for predation, defense and competition. The major venom component, conotoxin, has received significant attention because it is useful in neuroscience research, drug development and molecular diversity studies. In this study, we report the genomic characterization of nine conotoxin gene superfamilies from 18 Conus species and investigate the relationships among conotoxin gene structure, molecular evolution and diversity. The I1, I2, M, O2, O3, P, S, and T superfamily precursors all contain three exons and two introns, while A superfamily members contain two exons and one intron. The introns are conserved within a certain gene superfamily, and also conserved across different Conus species, but divergent among different superfamilies. The intronic sequences contain many simple repeat sequences and regulatory elements that may influence conotoxin gene expression. Furthermore, due to the unique gene structure of conotoxins, the base substitution rates and the number of positively selected sites vary greatly among exons. Many more point mutations and trinucleotide indels were observed in the mature peptide exon than in the other exons. In addition, the first example of alternative splicing in conotoxin genes was found. These results suggest that the diversity of conotoxin genes has been shaped by point mutations and indels, as well as rare gene recombination or alternative splicing events, and that the unique gene structures could have made a contribution to the evolution of conotoxin genes.

  14. Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences.

    PubMed

    Ishitani, Yoshiyuki; Kamikawa, Ryoma; Yabuki, Akinori; Tsuchiya, Masashi; Inagaki, Yuji; Takishita, Kiyotaka

    2012-01-01

    Elongation factor 1α (EF-1α) and elongation factor-like (EFL) proteins are considered to carry out equivalent functions in translation in eukaryotic cells. Elongation factor 1α and EFL genes are patchily distributed in the global eukaryotic tree, suggesting that the evolution of these elongation factors cannot be reconciled without multiple lateral gene transfer and/or ancestral co-occurrence followed by differential loss of either of the two factors. Our current understanding of the EF-1α/EFL evolution in the eukaryotic group Rhizaria, composed of Foraminifera, Radiolaria, Filosa, and Endomyxa, remains insufficient, as no information on EF-1α/EFL gene is available for any members of Radiolaria. In this study, EFL genes were experimentally isolated from four polycystine radiolarians (i.e. Dictyocoryne, Eucyrtidium, Collozoum, and Sphaerozoum), as well as retrieved from publicly accessible expressed sequence tag data of two acantharean radiolarians (i.e. Astrolonche and Phyllostaurus) and the endomyxan Gromia. The EFL homologs from radiolarians, foraminiferans, and Gromia formed a robust clade in both maximum-likelihood and Bayesian phylogenetic analyses, suggesting that EFL genes were vertically inherited from their common ancestor. We propose an updated model for EF-1α/EFL evolution in Rhizaria by incorporating new EFL data obtained in this study.

  15. The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution.

    PubMed

    Hill, Matthew M; Broman, Karl W; Stupka, Elia; Smith, William C; Jiang, Di; Sidow, Arend

    2008-08-01

    The urochordate Ciona savignyi is an emerging model organism for the study of chordate evolution, development, and gene regulation. The extreme level of polymorphism in its population has inspired novel approaches in genome assembly, which we here continue to develop. Specifically, we present the reconstruction of all of C. savignyi's chromosomes via the development of a comprehensive genetic map, without a physical map intermediate. The resulting genetic map is complete, having one linkage group for each one of the 14 chromosomes. Eighty-three percent of the reference genome sequence is covered. The chromosomal reconstruction allowed us to investigate the evolution of genome structure in highly polymorphic species, by comparing the genome of C. savignyi to its divergent sister species, Ciona intestinalis. Both genomes have been extensively reshaped by intrachromosomal rearrangements. Interchromosomal changes have been extremely rare. This is in striking contrast to what has been observed in vertebrates, where interchromosomal events are commonplace. These results, when considered in light of the neutral theory, suggest fundamentally different modes of evolution of animal species with large versus small population sizes.

  16. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.

    PubMed

    Sun, Yan-Bo; Xiong, Zi-Jun; Xiang, Xue-Yan; Liu, Shi-Ping; Zhou, Wei-Wei; Tu, Xiao-Long; Zhong, Li; Wang, Lu; Wu, Dong-Dong; Zhang, Bao-Lin; Zhu, Chun-Ling; Yang, Min-Min; Chen, Hong-Man; Li, Fang; Zhou, Long; Feng, Shao-Hong; Huang, Chao; Zhang, Guo-Jie; Irwin, David; Hillis, David M; Murphy, Robert W; Yang, Huan-Ming; Che, Jing; Wang, Jun; Zhang, Ya-Ping

    2015-03-17

    The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

  17. Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences.

    PubMed

    Ishitani, Yoshiyuki; Kamikawa, Ryoma; Yabuki, Akinori; Tsuchiya, Masashi; Inagaki, Yuji; Takishita, Kiyotaka

    2012-01-01

    Elongation factor 1α (EF-1α) and elongation factor-like (EFL) proteins are considered to carry out equivalent functions in translation in eukaryotic cells. Elongation factor 1α and EFL genes are patchily distributed in the global eukaryotic tree, suggesting that the evolution of these elongation factors cannot be reconciled without multiple lateral gene transfer and/or ancestral co-occurrence followed by differential loss of either of the two factors. Our current understanding of the EF-1α/EFL evolution in the eukaryotic group Rhizaria, composed of Foraminifera, Radiolaria, Filosa, and Endomyxa, remains insufficient, as no information on EF-1α/EFL gene is available for any members of Radiolaria. In this study, EFL genes were experimentally isolated from four polycystine radiolarians (i.e. Dictyocoryne, Eucyrtidium, Collozoum, and Sphaerozoum), as well as retrieved from publicly accessible expressed sequence tag data of two acantharean radiolarians (i.e. Astrolonche and Phyllostaurus) and the endomyxan Gromia. The EFL homologs from radiolarians, foraminiferans, and Gromia formed a robust clade in both maximum-likelihood and Bayesian phylogenetic analyses, suggesting that EFL genes were vertically inherited from their common ancestor. We propose an updated model for EF-1α/EFL evolution in Rhizaria by incorporating new EFL data obtained in this study. PMID:22672006

  18. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes

    PubMed Central

    Sun, Yan-Bo; Xiong, Zi-Jun; Xiang, Xue-Yan; Liu, Shi-Ping; Zhou, Wei-Wei; Tu, Xiao-Long; Zhong, Li; Wang, Lu; Wu, Dong-Dong; Zhang, Bao-Lin; Zhu, Chun-Ling; Yang, Min-Min; Chen, Hong-Man; Li, Fang; Zhou, Long; Feng, Shao-Hong; Huang, Chao; Zhang, Guo-Jie; Irwin, David; Hillis, David M.; Murphy, Robert W.; Yang, Huan-Ming; Che, Jing; Wang, Jun; Zhang, Ya-Ping

    2015-01-01

    The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies. PMID:25733869

  19. Age, distance, and geochemical evolution within a monogenetic volcanic field: Analyzing patterns in the Auckland Volcanic Field eruption sequence

    NASA Astrophysics Data System (ADS)

    Corvec, Nicolas Le; Bebbington, Mark S.; Lindsay, Jan M.; McGee, Lucy E.

    2013-09-01

    The Auckland Volcanic Field (AVF) is a young active monogenetic basaltic field, which contains ˜50 volcanoes scattered across the Auckland metropolitan area. Understanding the temporal, spatial, and chemical evolution of the AVF during the last c.a. 250 ka is crucial in order to forecast a future eruption. Recent studies have provided new age constraints and potential temporal sequences of the past eruptions within the AVF. We use this information to study how the spatial distribution of the volcanic centers evolves with time, and how the chemical composition of the erupted magmas evolves with time and space. We seek to develop a methodology which compares successive eruptions to describe the link between geochemical and spatiotemporal evolution of volcanic centers within a monogenetic volcanic field. This methodology is tested with the present day data of the AVF. The Poisson nearest neighbor analysis shows that the spatial behavior of the field has been constant overtime, with the spatial distribution of the volcanic centers fitting the Poisson model within the significance levels. The results of the meta-analysis show the existence of correlations between the chemical composition of the erupted magmas and distance, volume, and time. The apparent randomness of the spatiotemporal evolution of the volcanic centers observed at the surface is probably influenced by the activity of the source. The methodology developed in this study can be used to identify possible relationships between composition trends and volume, time and/or distance to the behavior of the source, for successive eruptions of the AVF.

  20. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.

    PubMed

    Sun, Yan-Bo; Xiong, Zi-Jun; Xiang, Xue-Yan; Liu, Shi-Ping; Zhou, Wei-Wei; Tu, Xiao-Long; Zhong, Li; Wang, Lu; Wu, Dong-Dong; Zhang, Bao-Lin; Zhu, Chun-Ling; Yang, Min-Min; Chen, Hong-Man; Li, Fang; Zhou, Long; Feng, Shao-Hong; Huang, Chao; Zhang, Guo-Jie; Irwin, David; Hillis, David M; Murphy, Robert W; Yang, Huan-Ming; Che, Jing; Wang, Jun; Zhang, Ya-Ping

    2015-03-17

    The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies. PMID:25733869

  1. Cambro-ordovician sea-level fluctuations and sequence boundaries: The missing record and the evolution of new taxa

    USGS Publications Warehouse

    Lehnert, O.; Miller, J.F.; Leslie, Stephen A.; Repetski, J.E.; Ethington, Raymond L.

    2005-01-01

    The evolution of early Palaeozoic conodont faunas shows a clear connection to sea-level changes. One way that this connection manifests itself is that thick successions of carbonates are missing beneath major sequence boundaries due to karstification and erosion. From this observation arises the question of how many taxa have been lost from different conodont lineages in these incomplete successions. Although many taxa suffered extinction due to the environmental stresses associated with falling sea-levels, some must have survived in these extreme conditions. The number of taxa missing in the early Palaeozoic tropics always will be unclear, but it will be even more difficult to evaluate the missing record in detrital successions of higher latitudes. A common pattern in the evolution of Cambrian-Ordovician conodont lineages is appearances of new species at sea-level rises and disappearances at sea-level drops. This simple picture can be complicated by intervals that consistently have no representatives of a particular lineage, even after extensive sampling of the most complete sections. Presumably the lineages survived in undocumented refugia. In this paper, we give examples of evolution in Cambrian-Ordovician shallowmarine conodont faunas and highlight problems of undiscovered or truly missing segments of lineages. ?? The Palaeontological Association.

  2. Directed evolution reveals requisite sequence elements in the functional expression of P450 2F1 in Escherichia coli.

    PubMed

    Behrendorff, James B Y H; Moore, Chad D; Kim, Keon-Hee; Kim, Dae-Hwan; Smith, Christopher A; Johnston, Wayne A; Yun, Chul-Ho; Yost, Garold S; Gillam, Elizabeth M J

    2012-09-17

    Cytochrome P450 2F1 (P450 2F1) is expressed exclusively in the human respiratory tract and is implicated in 3-methylindole (3MI)-induced pneumotoxicity via dehydrogenation of 3MI to a reactive electrophilic intermediate, 3-methyleneindolenine (3-MEI). Studies of P450 2F1 to date have been limited by the failure to express this enzyme in Escherichia coli. By contrast, P450 2F3, a caprine homologue that shares 84% sequence identity with P450 2F1 (86 amino acid differences), has been expressed in E. coli at yields greater than 250 nmol/L culture. We hypothesized that a limited number of sequence differences between P450s 2F1 and 2F3 could limit P450 2F1 expression in E. coli and that problematic P450 2F1 sequence elements could be identified by directed evolution. A library of P450 2F1/2F3 mutants was created by DNA family shuffling and screened for expression in E. coli. Three generations of DNA shuffling revealed a mutant (named JH_2F_F3_1_007) with 96.5% nucleotide sequence identity to P450 2F1 and which expressed 119 ± 40 pmol (n = 3, mean ± SD) hemoprotein in 1 mL microaerobic cultures. Across all three generations, two regions were observed where P450 2F3-derived sequence was consistently substituted for P450 2F1 sequence in expressing mutants, encoding nine amino acid differences between P450s 2F1 and 2F3: nucleotides 191-278 (amino acids 65-92) and 794-924 (amino acids 265-305). Chimeras constructed to specifically test the importance of these two regions confirmed that P450 2F3 sequence is essential in both regions for expression in E. coli but that other non-P450 2F1 sequence elements outside of these regions also improved the expression of mutant JH_2F_F3_1_007. Mutant JH_2F_F3_1_007 catalyzed the dehydrogenation of 3MI to 3-MEI as indicated by the observation of glutathione adducts after incubation in the presence of glutathione. The JH_2F_F3_1_007 protein differs from P450 2F1 at only 20 amino acids and should facilitate further studies of the structure

  3. HIV-1 sequence evolution in vivo after superinfection with three viral strains

    PubMed Central

    Kozaczynska, Karolina; Cornelissen, Marion; Reiss, Peter; Zorgdrager, Fokla; van der Kuyl, Antoinette C

    2007-01-01

    With millions of people infected worldwide, the evolution of HIV-1 in vivo has been the subject of much research. Although recombinant viruses were detected early in the epidemic, evidence that HIV-1 dual infections really occurred came much later. Dual infected patients, consisting of coinfected (second infection before seroconversion) and superinfected (second infection after seroconversion) individuals, opened up a new area of HIV-1 evolution studies. Here, we describe the in-depth analysis of HIV-1 over time in a patient twice superinfected with HIV-1, first with a subtype B (B2) strain and then with CRF01_AE after initial infection with a subtype B (B1) strain. The nucleotide evolution of gag and env-V3 of the three strains followed a similar pattern: a very low substitution rate in the first 2–3 years of infection, with an increase in synonymous substitutions thereafter. Convergent evolution at the protein level was rare: only a single amino acid in a gag p24 epitope showed convergence in the subtype B strains. Reversal of CTL-epitope mutations were also rare, and did not converge. Recombinant viruses were observed between the two subtype B strains. Luciferase-assays suggested that the CRF01_AE long terminal repeat (LTR) constituted the strongest promoter, but this was not reflected in the plasma viral load. Specific real-time PCR assays based upon the env gene showed that strain B2 and CRF01_AE RNA was present in equal amounts, while levels of strain B1 were 100-fold lower. All three strains were detected in seminal plasma, suggesting that simultaneous transmission is possible. PMID:17716368

  4. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts

    PubMed Central

    Liu, Zhanjiang; Liu, Shikai; Yao, Jun; Bao, Lisui; Zhang, Jiaren; Li, Yun; Jiang, Chen; Sun, Luyang; Wang, Ruijia; Zhang, Yu; Zhou, Tao; Zeng, Qifan; Fu, Qiang; Gao, Sen; Li, Ning; Koren, Sergey; Jiang, Yanliang; Zimin, Aleksey; Xu, Peng; Phillippy, Adam M.; Geng, Xin; Song, Lin; Sun, Fanyue; Li, Chao; Wang, Xiaozhu; Chen, Ailu; Jin, Yulin; Yuan, Zihao; Yang, Yujia; Tan, Suxu; Peatman, Eric; Lu, Jianguo; Qin, Zhenkui; Dunham, Rex; Li, Zhaoxia; Sonstegard, Tad; Feng, Jianbin; Danzmann, Roy G.; Schroeder, Steven; Scheffler, Brian; Duke, Mary V.; Ballard, Linda; Kucuktas, Huseyin; Kaltenboeck, Ludmilla; Liu, Haixia; Armbruster, Jonathan; Xie, Yangjie; Kirby, Mona L.; Tian, Yi; Flanagan, Mary Elizabeth; Mu, Weijie; Waldbieser, Geoffrey C.

    2016-01-01

    Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance. PMID:27249958

  5. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic and genomic analyses of Upland cotton (Gossypium hirsutum) are difficult because it has a complex allotetraploid (AADD; 2n = 4x = 52) genome. Here we sequenced, assembled and analyzed the world's most important cultivated cotton genome with 246.2 gigabase (Gb) clean data obtained using whol...

  6. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.

    PubMed

    Liu, Zhanjiang; Liu, Shikai; Yao, Jun; Bao, Lisui; Zhang, Jiaren; Li, Yun; Jiang, Chen; Sun, Luyang; Wang, Ruijia; Zhang, Yu; Zhou, Tao; Zeng, Qifan; Fu, Qiang; Gao, Sen; Li, Ning; Koren, Sergey; Jiang, Yanliang; Zimin, Aleksey; Xu, Peng; Phillippy, Adam M; Geng, Xin; Song, Lin; Sun, Fanyue; Li, Chao; Wang, Xiaozhu; Chen, Ailu; Jin, Yulin; Yuan, Zihao; Yang, Yujia; Tan, Suxu; Peatman, Eric; Lu, Jianguo; Qin, Zhenkui; Dunham, Rex; Li, Zhaoxia; Sonstegard, Tad; Feng, Jianbin; Danzmann, Roy G; Schroeder, Steven; Scheffler, Brian; Duke, Mary V; Ballard, Linda; Kucuktas, Huseyin; Kaltenboeck, Ludmilla; Liu, Haixia; Armbruster, Jonathan; Xie, Yangjie; Kirby, Mona L; Tian, Yi; Flanagan, Mary Elizabeth; Mu, Weijie; Waldbieser, Geoffrey C

    2016-01-01

    Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance. PMID:27249958

  7. Application of seismic sequence concepts to basin evolution and petroleum exploration, Pletmos basin, offshore South Africa

    SciTech Connect

    Keenan, J.H.G. )

    1989-03-01

    As a result of excellent seismic data, shallow burial depths, and slow subsidence rates, 67 type 1 and type 2 unconformities were identified in the postrift Cretaceous section of the Pletmos subbasins. The purpose of this study was to develop a seismic sequence-stratigraphic framework for the mid-Valanginian to mid-Campanian sequences as a basis for future petroleum exploration. The study further developed the recent stratigraphic techniques proposed by Exxon. Sixteen of the 67 type 1 and type 2 unconformities could be correlated directly with Exxon's global third-order cycles; the remaining 51, interpreted to be fourth- and fifth-order cycles, could be grouped into megasequences comprising 2 to 6 sequences, bounded by major third-order type 1 unconformities. The study demonstrates the complex interplay of variations in sea level fluctuation, differential subsidence rates, sediment supply, and tectonic stability and the resultant wide range of geometries and styles in depositional environments. By using seismic sequence concepts, these variables can be accounted for and can be made with greater assurance. Further analyses of lowstand systems tracts are underway to localize stratigraphic trap prospects to be drilled in the near future.

  8. Rethinking the Undergraduate Public Relations Sequence: Evolution of Thought 1975-1995.

    ERIC Educational Resources Information Center

    Fischer, Rick

    Public relations sequence heads have the luxury of a strong and supportive foundation on which to build a program of instruction. The field has a rich collection of thinking and recommendations relating to public relations education. The Association for Education in Journalism (AEJ) and the Public Relations Society of America (PRSA) conducted a…

  9. Identifying Learning Behaviors by Contextualizing Differential Sequence Mining with Action Features and Performance Evolution

    ERIC Educational Resources Information Center

    Kinnebrew, John S.; Biswas, Gautam

    2012-01-01

    Our learning-by-teaching environment, Betty's Brain, captures a wealth of data on students' learning interactions as they teach a virtual agent. This paper extends an exploratory data mining methodology for assessing and comparing students' learning behaviors from these interaction traces. The core algorithm employs sequence mining techniques to…

  10. Delayed Gratification Habitable Zones: When Deep Outer Solar System Regions Become Balmy During Post-Main Sequence Stellar Evolution

    NASA Astrophysics Data System (ADS)

    Stern, S. Alan

    2003-06-01

    Like all low- and moderate-mass stars, the Sun will burn as a red giant during its later evolution, generating of solar luminosities for some tens of millions of years. During this post-main sequence phase, the habitable (i.e., liquid water) thermal zone of our Solar System will lie in the region where Triton, Pluto-Charon, and Kuiper Belt objects orbit. Compared with the 1 AU habitable zone where Earth resides, this "delayed gratification habitable zone" (DGHZ) will enjoy a far less biologically hazardous environment - with lower harmful radiation levels from the Sun, and a far less destructive collisional environment. Objects like Triton, Pluto-Charon, and Kuiper Belt objects, which are known to be rich in both water and organics, will then become possible sites for biochemical and perhaps even biological evolution. The Kuiper Belt, with >105 objects >=50 km in radius and more than three times the combined surface area of the four terrestrial planets, provides numerous sites for possible evolution once the Sun's DGHZ reaches it. The Sun's DGHZ might be thought to only be of academic interest owing to its great separation from us in time. However, ~109 Milky Way stars burn as luminous red giants today. Thus, if icy-organic objects are common in the 20-50 AU zones of these stars, as they are in our Solar System (and as inferred in numerous main sequence stellar disk systems), then DGHZs may form a niche type of habitable zone that is likely to be numerically common in the Galaxy.

  11. Delayed gratification habitable zones: when deep outer solar system regions become balmy during post-main sequence stellar evolution.

    PubMed

    Stern, S Alan

    2003-01-01

    Like all low- and moderate-mass stars, the Sun will burn as a red giant during its later evolution, generating of solar luminosities for some tens of millions of years. During this post-main sequence phase, the habitable (i.e., liquid water) thermal zone of our Solar System will lie in the region where Triton, Pluto-Charon, and Kuiper Belt objects orbit. Compared with the 1 AU habitable zone where Earth resides, this "delayed gratification habitable zone" (DGHZ) will enjoy a far less biologically hazardous environment - with lower harmful radiation levels from the Sun, and a far less destructive collisional environment. Objects like Triton, Pluto-Charon, and Kuiper Belt objects, which are known to be rich in both water and organics, will then become possible sites for biochemical and perhaps even biological evolution. The Kuiper Belt, with >10(5) objects > or =50 km in radius and more than three times the combined surface area of the four terrestrial planets, provides numerous sites for possible evolution once the Sun's DGHZ reaches it. The Sun's DGHZ might be thought to only be of academic interest owing to its great separation from us in time. However, approximately 10(9) Milky Way stars burn as luminous red giants today. Thus, if icy-organic objects are common in the 20-50 AU zones of these stars, as they are in our Solar System (and as inferred in numerous main sequence stellar disk systems), then DGHZs may form a niche type of habitable zone that is likely to be numerically common in the Galaxy.

  12. Delayed gratification habitable zones: when deep outer solar system regions become balmy during post-main sequence stellar evolution.

    PubMed

    Stern, S Alan

    2003-01-01

    Like all low- and moderate-mass stars, the Sun will burn as a red giant during its later evolution, generating of solar luminosities for some tens of millions of years. During this post-main sequence phase, the habitable (i.e., liquid water) thermal zone of our Solar System will lie in the region where Triton, Pluto-Charon, and Kuiper Belt objects orbit. Compared with the 1 AU habitable zone where Earth resides, this "delayed gratification habitable zone" (DGHZ) will enjoy a far less biologically hazardous environment - with lower harmful radiation levels from the Sun, and a far less destructive collisional environment. Objects like Triton, Pluto-Charon, and Kuiper Belt objects, which are known to be rich in both water and organics, will then become possible sites for biochemical and perhaps even biological evolution. The Kuiper Belt, with >10(5) objects > or =50 km in radius and more than three times the combined surface area of the four terrestrial planets, provides numerous sites for possible evolution once the Sun's DGHZ reaches it. The Sun's DGHZ might be thought to only be of academic interest owing to its great separation from us in time. However, approximately 10(9) Milky Way stars burn as luminous red giants today. Thus, if icy-organic objects are common in the 20-50 AU zones of these stars, as they are in our Solar System (and as inferred in numerous main sequence stellar disk systems), then DGHZs may form a niche type of habitable zone that is likely to be numerically common in the Galaxy. PMID:14577880

  13. Long-term trends in evolution of indels in protein sequences

    PubMed Central

    Wolf, Yuri; Madej, Thomas; Babenko, Vladimir; Shoemaker, Benjamin; Panchenko, Anna R

    2007-01-01

    Background In this paper we describe an analysis of the size evolution of both protein domains and their indels, as inferred by changing sizes of whole domains or individual unaligned regions or "spacers". We studied relatively early evolutionary events and focused on protein domains which are conserved among various taxonomy groups. Results We found that more than one third of all domains have a statistically significant tendency to increase/decrease in size in evolution as judged from the overall domain size distribution as well as from the size distribution of individual spacers. Moreover, the fraction of domains and individual spacers increasing in size is almost twofold larger than the fraction decreasing in size. Conclusion We showed that the tolerance to insertion and deletion events depends on the domain's taxonomy span. Eukaryotic domains are depleted in insertions compared to the overall test set, namely, the number of spacers increasing in size is about the same as the number of spacers decreasing in size. On the other hand, ancient domain families show some bias towards insertions or spacers which grow in size in evolution. Domains from several Gene Ontology categories also demonstrate certain tendencies for insertion or deletion events as inferred from the analysis of spacer sizes. PMID:17298668

  14. Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.

    PubMed

    Warren, Jessica M; Simmons, Mark P; Wu, Zhiqiang; Sloan, Daniel B

    2016-01-11

    The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses.

  15. Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.

    PubMed

    Warren, Jessica M; Simmons, Mark P; Wu, Zhiqiang; Sloan, Daniel B

    2016-02-01

    The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses. PMID:26759362

  16. Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes

    PubMed Central

    Warren, Jessica M.; Simmons, Mark P.; Wu, Zhiqiang; Sloan, Daniel B.

    2016-01-01

    The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses. PMID:26759362

  17. Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas.

    PubMed

    Sri, Tanu; Mayee, Pratiksha; Singh, Anandita

    2015-09-01

    Whole genome sequence analyses allow unravelling such evolutionary consequences of meso-triplication event in Brassicaceae (∼14-20 million years ago (MYA)) as differential gene fractionation and diversification in homeologous sub-genomes. This study presents a simple gene-centric approach involving microsynteny and natural genetic variation analysis for understanding SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1) homeolog evolution in Brassica. Analysis of microsynteny in Brassica rapa homeologous regions containing SOC1 revealed differential gene fractionation correlating to reported fractionation status of sub-genomes of origin, viz. least fractionated (LF), moderately fractionated 1 (MF1) and most fractionated (MF2), respectively. Screening 18 cultivars of 6 Brassica species led to the identification of 8 genomic and 27 transcript variants of SOC1, including splice-forms. Co-occurrence of both interrupted and intronless SOC1 genes was detected in few Brassica species. In silico analysis characterised Brassica SOC1 as MADS intervening, K-box, C-terminal (MIKC(C)) transcription factor, with highly conserved MADS and I domains relative to K-box and C-terminal domain. Phylogenetic analyses and multiple sequence alignments depicting shared pattern of silent/non-silent mutations assigned Brassica SOC1 homologs into groups based on shared diploid base genome. In addition, a sub-genome structure in uncharacterised Brassica genomes was inferred. Expression analysis of putative MF2 and LF (Brassica diploid base genome A (AA)) sub-genome-specific SOC1 homeologs of Brassica juncea revealed near identical expression pattern. However, MF2-specific homeolog exhibited significantly higher expression implying regulatory diversification. In conclusion, evidence for polyploidy-induced sequence and regulatory evolution in Brassica SOC1 is being presented wherein differential homeolog expression is implied in functional diversification.

  18. Tracking the evolution of sex chromosome systems in Melanoplinae grasshoppers through chromosomal mapping of repetitive DNA sequences

    PubMed Central

    2013-01-01

    Background The accumulation of repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems. Results Our data indicate a non-spreading of heterochromatic blocks and pool of repetitive DNAs (C0t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. Conclusions These results suggest a common origin and subsequent differential accumulation of repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for repetitive DNAs in the diversification of sex chromosome systems in grasshoppers. PMID:23937327

  19. Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas.

    PubMed

    Sri, Tanu; Mayee, Pratiksha; Singh, Anandita

    2015-09-01

    Whole genome sequence analyses allow unravelling such evolutionary consequences of meso-triplication event in Brassicaceae (∼14-20 million years ago (MYA)) as differential gene fractionation and diversification in homeologous sub-genomes. This study presents a simple gene-centric approach involving microsynteny and natural genetic variation analysis for understanding SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1) homeolog evolution in Brassica. Analysis of microsynteny in Brassica rapa homeologous regions containing SOC1 revealed differential gene fractionation correlating to reported fractionation status of sub-genomes of origin, viz. least fractionated (LF), moderately fractionated 1 (MF1) and most fractionated (MF2), respectively. Screening 18 cultivars of 6 Brassica species led to the identification of 8 genomic and 27 transcript variants of SOC1, including splice-forms. Co-occurrence of both interrupted and intronless SOC1 genes was detected in few Brassica species. In silico analysis characterised Brassica SOC1 as MADS intervening, K-box, C-terminal (MIKC(C)) transcription factor, with highly conserved MADS and I domains relative to K-box and C-terminal domain. Phylogenetic analyses and multiple sequence alignments depicting shared pattern of silent/non-silent mutations assigned Brassica SOC1 homologs into groups based on shared diploid base genome. In addition, a sub-genome structure in uncharacterised Brassica genomes was inferred. Expression analysis of putative MF2 and LF (Brassica diploid base genome A (AA)) sub-genome-specific SOC1 homeologs of Brassica juncea revealed near identical expression pattern. However, MF2-specific homeolog exhibited significantly higher expression implying regulatory diversification. In conclusion, evidence for polyploidy-induced sequence and regulatory evolution in Brassica SOC1 is being presented wherein differential homeolog expression is implied in functional diversification. PMID:26276216

  20. Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma.

    PubMed

    Vernon, D; Gutell, R R; Cannone, J J; Rumpf, R W; Birky, C W

    2001-09-01

    Polytoma obtusum and Polytoma uvella are members of a clade of nonphotosynthetic chlorophyte algae closely related to Chlamydomonas humicola and other photosynthetic members of the Chlamydomonadaceae. Descended from a nonphotosynthetic mutant, these obligate heterotrophs retain a plastid (leucoplast) with a functional protein synthetic system, and a plastid genome (lpDNA) with functional genes encoding proteins required for transcription and translation. Comparative studies of the evolution of genes in chloroplasts and leucoplasts can identify modes of selection acting on the plastid genome. Two plastid genes--rrn16, encoding the plastid small-subunit rRNA, and tufA, encoding elongation factor Tu--retain their functions in protein synthesis after the loss of photosynthesis in two nonphotosynthetic Polytoma clades but show a substantially accelerated rate of base substitution in the P. uvella clade. The accelerated evolution of tufA is due, at least partly, to relaxed codon bias favoring codons that can be read without wobble, mainly in three amino acids. Selection for these codons may be relaxed because leucoplasts are required to synthesize fewer protein molecules per unit time than are chloroplasts (reduced protein synthetic load) and thus require a lower rate of synthesis of elongation factor Tu. Relaxed selection due to a lower protein synthetic load is also a plausible explanation for the accelerated rate of evolution of rrn16, but the available data are insufficient to test the hypothesis for this gene. The tufA and rrn16 genes in Polytoma oviforme, the sole member of a second nonphotosynthetic clade, are also functional but show no sign of relaxed selection.

  1. The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolution.

    PubMed

    Deeb, Samir S; Wakefield, Matthew J; Tada, Takashi; Marotte, Lauren; Yokoyama, Shozo; Marshall Graves, Jenny A

    2003-10-01

    Studies on marsupial color vision have been limited to very few species. There is evidence from behavioral, electroretinographic (ERG), and microspectrophotometric (MSP) measurements for the existence of both dichromatic and trichromatic color vision. No studies have yet investigated the molecular mechanisms of spectral tuning in the visual pigments of marsupials. Our study is the first to determine the mRNA sequence, infer the amino acid sequence, and determine, by in vitro expression, the spectra of the cone opsins of a marsupial, the tammar wallaby (Macropus eugenii). This yielded some information on mechanisms and evolution of spectral tuning of these pigments. The tammar wallaby retina contains only short-wavelength sensitive (SWS) and middle-wavelength sensitive (MWS) pigment mRNAs. This predicts dichromatic color vision, which is consistent with conclusions from previous behavioral studies ( Hemmi 1999). We found that the wallaby has a SWS1 class pigment of 346 amino acids. Sequence comparison with eutherian SWS pigments predicts that this SWS1 pigment absorbs maximally (lambdamax) at 424 nm and, therefore, is a blue rather than a UV pigment. This (lambdamax) is close to that of the in vitro-expressed wallaby SWS pigment (lambdamax of 420 +/- 2 nm) and to that determined behaviorally (420 nm). The difference from the mouse UV pigment (lambdamax of 359 nm) is largely accounted for by the F86Y substitution, in agreement with in vitro results comparing a variety of other SWS pigments. This suggests that spectral tuning employing F86Y substitution most likely arose independently in the marsupials and ungulates as a result of convergent evolution. An apparently different mechanism of spectral tuning of the SWS1 pigments, involving five amino acid positions, evolved in primates. The wallaby MWS pigment has 363 amino acids. Species comparisons at positions critical to spectral tuning predict a lambdamax near 530 nm, which is close to that of the in vitro

  2. The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolution.

    PubMed

    Deeb, Samir S; Wakefield, Matthew J; Tada, Takashi; Marotte, Lauren; Yokoyama, Shozo; Marshall Graves, Jenny A

    2003-10-01

    Studies on marsupial color vision have been limited to very few species. There is evidence from behavioral, electroretinographic (ERG), and microspectrophotometric (MSP) measurements for the existence of both dichromatic and trichromatic color vision. No studies have yet investigated the molecular mechanisms of spectral tuning in the visual pigments of marsupials. Our study is the first to determine the mRNA sequence, infer the amino acid sequence, and determine, by in vitro expression, the spectra of the cone opsins of a marsupial, the tammar wallaby (Macropus eugenii). This yielded some information on mechanisms and evolution of spectral tuning of these pigments. The tammar wallaby retina contains only short-wavelength sensitive (SWS) and middle-wavelength sensitive (MWS) pigment mRNAs. This predicts dichromatic color vision, which is consistent with conclusions from previous behavioral studies ( Hemmi 1999). We found that the wallaby has a SWS1 class pigment of 346 amino acids. Sequence comparison with eutherian SWS pigments predicts that this SWS1 pigment absorbs maximally (lambdamax) at 424 nm and, therefore, is a blue rather than a UV pigment. This (lambdamax) is close to that of the in vitro-expressed wallaby SWS pigment (lambdamax of 420 +/- 2 nm) and to that determined behaviorally (420 nm). The difference from the mouse UV pigment (lambdamax of 359 nm) is largely accounted for by the F86Y substitution, in agreement with in vitro results comparing a variety of other SWS pigments. This suggests that spectral tuning employing F86Y substitution most likely arose independently in the marsupials and ungulates as a result of convergent evolution. An apparently different mechanism of spectral tuning of the SWS1 pigments, involving five amino acid positions, evolved in primates. The wallaby MWS pigment has 363 amino acids. Species comparisons at positions critical to spectral tuning predict a lambdamax near 530 nm, which is close to that of the in vitro

  3. High Power Beam Test and Measurement of Emittance Evolution of a 1.6-Cell Photocathode RF Gun at Pohang Accelerator Laboratory

    NASA Astrophysics Data System (ADS)

    Park, Jang-Ho; Park, Sung-Ju; Kim, Changbum; Parc, Yong-Woon; Hong, Ju-Ho; Huang, Jung-Yun; Xiang, Dao; Wang, Xijie; Ko, In Soo

    2007-04-01

    A Brookhaven National Laboratory (BNL) GUN-IV type photocathode rf gun has been fabricated to use in femtosecond electron diffraction (FED), femtosecond far infrared radiation (fs-FIR) facility, and X-ray free electron laser (XFEL) facilities at the Pohang Accelerator Laboratory (PAL). The gun consists of a 1.6-cell cavity with a copper cathode, a solenoid magnet, beam diagnostic components and auxiliary systems. We report here the measurement of the basic beam parameters which confirm a successful fabrication of the photocathode RF gun system. The emittance evolution is measured by an emittance meter and compared with the PARMELA simulation, which shows a good agreement.

  4. First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution.

    PubMed

    Smith, David Roy; Kayal, Ehsan; Yanagihara, Angel A; Collins, Allen G; Pirro, Stacy; Keeling, Patrick J

    2012-01-01

    Animal mitochondrial DNAs (mtDNAs) are typically single circular chromosomes, with the exception of those from medusozoan cnidarians (jellyfish and hydroids), which are linear and sometimes fragmented. Most medusozoans have linear monomeric or linear bipartite mitochondrial genomes, but preliminary data have suggested that box jellyfish (cubozoans) have mtDNAs that consist of many linear chromosomes. Here, we present the complete mtDNA sequence from the winged box jellyfish Alatina moseri (the first from a cubozoan). This genome contains unprecedented levels of fragmentation: 18 unique genes distributed over eight 2.9- to 4.6-kb linear chromosomes. The telomeres are identical within and between chromosomes, and recombination between subtelomeric sequences has led to many genes initiating or terminating with sequences from other genes (the most extreme case being 150 nt of a ribosomal RNA containing the 5' end of nad2), providing evidence for a gene conversion-based model of telomere evolution. The silent-site nucleotide variation within the A. moseri mtDNA is among the highest observed from a eukaryotic genome and may be associated with elevated rates of recombination. PMID:22117085

  5. Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA.

    PubMed

    Kehie, Mechuselie; Kumaria, Suman; Devi, Khumuckcham Sangeeta; Tandon, Pramod

    2016-02-01

    Sequences of the Internal Transcribed Spacer (ITS1-5.8S-ITS2) of nuclear ribosomal DNAs were explored to study the genetic diversity and molecular evolution of Naga King Chili. Our study indicated the occurrence of nucleotide polymorphism and haplotypic diversity in the ITS regions. The present study demonstrated that the variability of ITS1 with respect to nucleotide diversity and sequence polymorphism exceeded that of ITS2. Sequence analysis of 5.8S gene revealed a much conserved region in all the accessions of Naga King Chili. However, strong phylogenetic information of this species is the distinct 13 bp deletion in the 5.8S gene which discriminated Naga King Chili from the rest of the Capsicum sp. Neutrality test results implied a neutral variation, and population seems to be evolving at drift-mutation equilibrium and free from directed selection pressure. Furthermore, mismatch analysis showed multimodal curve indicating a demographic equilibrium. Phylogenetic relationships revealed by Median Joining Network (MJN) analysis denoted a clear discrimination of Naga King Chili from its closest sister species (Capsicum chinense and Capsicum frutescens). The absence of star-like network of haplotypes suggested an ancient population expansion of this chili. PMID:26862481

  6. Sequence, evolution and tissue expression patterns of an epidermal type I keratin from the shark Scyliorhinus stellaris.

    PubMed

    Schaffeld, Michael; Höffling, Simon; Jürgen, Markl

    2004-08-01

    From the shark Scyliorhinus stellaris we cloned and sequenced a cDNA encoding a novel type I keratin, termed SstK10. By MALDI-MS peptide mass fingerprinting of cytoskeletal proteins separated on polyacrylamide gels, we assigned SstK10 to a 46-kDa protein which is the major epidermal type I ("IE") keratin in this fish and is specifically expressed in stratified epithelia. In a phylogenetic tree based on type I keratin sequences and with lamprey keratins applied as outgroup, SstK10 branches off in a rather basal position. This tree strongly supports the concept that teleost keratins and tetrapod keratins resulted from two independent gene radiation processes. The only exception is human K18 because its orthologs have been found in all jawed vertebrates (Gnathostomata) studied; in the tree, they form a common, most early branch, with the shark version, SstK18, in the most basal position. Thus, the sequences of SstK10 and SstK18 also favor the classical view of vertebrate evolution that considers the cartilaginous fishes as the most ancient living Gnathostomata. To determine the overall expression patterns of epidermal ("E") and simple epithelial ("S") keratins in this shark, we furthermore tested a panel of monoclonal anti-keratin antibodies by immunofluorescence microscopy of frozen tissue sections, and in immunoblots of cytoskeletal preparations, demonstrating that immunodetection of specific keratins is a convenient method to characterize epithelial tissues in shark.

  7. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

    PubMed

    Alverson, Andrew J; Wei, XiaoXin; Rice, Danny W; Stern, David B; Barry, Kerrie; Palmer, Jeffrey D

    2010-06-01

    The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content. The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA. The large size of the Cucurbita mitochondrial genome reflects the accumulation of unprecedented amounts of both chloroplast sequences (>113 kb) and short repeated sequences (>370 kb). A low mutation rate has been hypothesized to underlie increases in both genome size and RNA editing frequency in plant mitochondria. However, despite its much larger genome, Cucurbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrullus but comparable levels of RNA editing. The evolution of mutation rate, genome size, and RNA editing are apparently decoupled in Cucurbitaceae, reflecting either simple stochastic variation or governance by different factors.

  8. Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA

    PubMed Central

    Kehie, Mechuselie; Kumaria, Suman; Devi, Khumuckcham Sangeeta; Tandon, Pramod

    2015-01-01

    Sequences of the Internal Transcribed Spacer (ITS1-5.8S-ITS2) of nuclear ribosomal DNAs were explored to study the genetic diversity and molecular evolution of Naga King Chili. Our study indicated the occurrence of nucleotide polymorphism and haplotypic diversity in the ITS regions. The present study demonstrated that the variability of ITS1 with respect to nucleotide diversity and sequence polymorphism exceeded that of ITS2. Sequence analysis of 5.8S gene revealed a much conserved region in all the accessions of Naga King Chili. However, strong phylogenetic information of this species is the distinct 13 bp deletion in the 5.8S gene which discriminated Naga King Chili from the rest of the Capsicum sp. Neutrality test results implied a neutral variation, and population seems to be evolving at drift–mutation equilibrium and free from directed selection pressure. Furthermore, mismatch analysis showed multimodal curve indicating a demographic equilibrium. Phylogenetic relationships revealed by Median Joining Network (MJN) analysis denoted a clear discrimination of Naga King Chili from its closest sister species (Capsicumchinense and Capsicumfrutescens). The absence of star-like network of haplotypes suggested an ancient population expansion of this chili. PMID:26862481

  9. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species.

    PubMed

    Kim, Seungill; Park, Minkyu; Yeom, Seon-In; Kim, Yong-Min; Lee, Je Min; Lee, Hyun-Ah; Seo, Eunyoung; Choi, Jaeyoung; Cheong, Kyeongchae; Kim, Ki-Tae; Jung, Kyongyong; Lee, Gir-Won; Oh, Sang-Keun; Bae, Chungyun; Kim, Saet-Byul; Lee, Hye-Young; Kim, Shin-Young; Kim, Myung-Shin; Kang, Byoung-Cheorl; Jo, Yeong Deuk; Yang, Hee-Bum; Jeong, Hee-Jin; Kang, Won-Hee; Kwon, Jin-Kyung; Shin, Chanseok; Lim, Jae Yun; Park, June Hyun; Huh, Jin Hoe; Kim, June-Sik; Kim, Byung-Dong; Cohen, Oded; Paran, Ilan; Suh, Mi Chung; Lee, Saet Buyl; Kim, Yeon-Ki; Shin, Younhee; Noh, Seung-Jae; Park, Junhyung; Seo, Young Sam; Kwon, Suk-Yoon; Kim, Hyun A; Park, Jeong Mee; Kim, Hyun-Jin; Choi, Sang-Bong; Bosland, Paul W; Reeves, Gregory; Jo, Sung-Hwan; Lee, Bong-Woo; Cho, Hyung-Taeg; Choi, Hee-Seung; Lee, Min-Soo; Yu, Yeisoo; Do Choi, Yang; Park, Beom-Seok; van Deynze, Allen; Ashrafi, Hamid; Hill, Theresa; Kim, Woo Taek; Pai, Hyun-Sook; Ahn, Hee Kyung; Yeam, Inhwa; Giovannoni, James J; Rose, Jocelyn K C; Sørensen, Iben; Lee, Sang-Jik; Kim, Ryan W; Choi, Ik-Young; Choi, Beom-Soon; Lim, Jong-Sung; Lee, Yong-Hwan; Choi, Doil

    2014-03-01

    Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.

  10. Sequence and evolution of the blue cone pigment gene in old and new world primates

    SciTech Connect

    Hunt, D.M.; Cowing, J.A.; Patel, R.

    1995-06-10

    The sequences of the blue cone photopigments in the talapoin monkey (Miopithecus talapoin), an Old World primate, and in the marmoset (Callithrix jacchus), a New World monkey, are presented. Both genes are composed of 5 exons separated by 4 introns. In this respect, they are identical to the human blue gene, and intron sizes are also similar. Based on the level of amino acid identity, both monkey pigments are members of the S branch of pigments. Alignment of these sequences with the human gene requires the insertion/deletion of two separate codons in exon 1. The silent site divergence between these primate blue genes indicates a separation of the Old and New World primate lineages around 43 million years ago. 41 refs., 1 fig., 3 tabs.

  11. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species.

    PubMed

    Kim, Seungill; Park, Minkyu; Yeom, Seon-In; Kim, Yong-Min; Lee, Je Min; Lee, Hyun-Ah; Seo, Eunyoung; Choi, Jaeyoung; Cheong, Kyeongchae; Kim, Ki-Tae; Jung, Kyongyong; Lee, Gir-Won; Oh, Sang-Keun; Bae, Chungyun; Kim, Saet-Byul; Lee, Hye-Young; Kim, Shin-Young; Kim, Myung-Shin; Kang, Byoung-Cheorl; Jo, Yeong Deuk; Yang, Hee-Bum; Jeong, Hee-Jin; Kang, Won-Hee; Kwon, Jin-Kyung; Shin, Chanseok; Lim, Jae Yun; Park, June Hyun; Huh, Jin Hoe; Kim, June-Sik; Kim, Byung-Dong; Cohen, Oded; Paran, Ilan; Suh, Mi Chung; Lee, Saet Buyl; Kim, Yeon-Ki; Shin, Younhee; Noh, Seung-Jae; Park, Junhyung; Seo, Young Sam; Kwon, Suk-Yoon; Kim, Hyun A; Park, Jeong Mee; Kim, Hyun-Jin; Choi, Sang-Bong; Bosland, Paul W; Reeves, Gregory; Jo, Sung-Hwan; Lee, Bong-Woo; Cho, Hyung-Taeg; Choi, Hee-Seung; Lee, Min-Soo; Yu, Yeisoo; Do Choi, Yang; Park, Beom-Seok; van Deynze, Allen; Ashrafi, Hamid; Hill, Theresa; Kim, Woo Taek; Pai, Hyun-Sook; Ahn, Hee Kyung; Yeam, Inhwa; Giovannoni, James J; Rose, Jocelyn K C; Sørensen, Iben; Lee, Sang-Jik; Kim, Ryan W; Choi, Ik-Young; Choi, Beom-Soon; Lim, Jong-Sung; Lee, Yong-Hwan; Choi, Doil

    2014-03-01

    Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species. PMID:24441736

  12. Type III polyketide synthase repertoire in Zingiberaceae: computational insights into the sequence, structure and evolution.

    PubMed

    Mallika, Vijayanathan; Aiswarya, Girija; Gincy, Paily Thottathil; Remakanthan, Appukuttan; Soniya, Eppurathu Vasudevan

    2016-07-01

    Zingiberaceae or 'ginger family' is the largest family in the order 'Zingiberales' with more than 1300 species in 52 genera, which are mostly distributed throughout Asia, tropical Africa and the native regions of America with their maximum diversity in Southeast Asia. Many of the members are important spice, medicinal or ornamental plants including ginger, turmeric, cardamom and kaempferia. These plants are distinguished for the highly valuable metabolic products, which are synthesised through phenylpropanoid pathway, where type III polyketide synthase is the key enzyme. In our present study, we used sequence, structural and evolutionary approaches to scrutinise the type III polyketide synthase (PKS) repertoire encoded in the Zingiberaceae family. Highly conserved amino acid residues in the sequence alignment and phylogram suggested strong relationships between the type III PKS members of Zingiberaceae. Sequence and structural level investigation of type III PKSs showed a small number of variations in the substrate binding pocket, leading to functional divergence among these PKS members. Molecular evolutionary studies indicate that type III PKSs within Zingiberaceae evolved under strong purifying selection pressure, and positive selections were rarely detected in the family. Structural modelling and protein-small molecule interaction studies on Zingiber officinale PKS 'a representative from Zingiberaceae' suggested that the protein is comparatively stable without much disorder and exhibited wide substrate acceptance.

  13. The impact of the neisserial DNA uptake sequences on genome evolution and stability

    PubMed Central

    Treangen, Todd J; Ambur, Ole Herman; Tonjum, Tone; Rocha, Eduardo PC

    2008-01-01

    Background Efficient natural transformation in Neisseria requires the presence of short DNA uptake sequences (DUSs). Doubts remain whether DUSs propagate by pure selfish molecular drive or are selected for 'safe sex' among conspecifics. Results Six neisserial genomes were aligned to identify gene conversion fragments, DUS distribution, spacing, and conservation. We found a strong link between recombination and DUS: DUS spacing matches the size of conversion fragments; genomes with shorter conversion fragments have more DUSs and more conserved DUSs; and conversion fragments are enriched in DUSs. Many recent and singly occurring DUSs exhibit too high divergence with homologous sequences in other genomes to have arisen by point mutation, suggesting their appearance by recombination. DUSs are over-represented in the core genome, under-represented in regions under diversification, and absent in both recently acquired genes and recently lost core genes. This suggests that DUSs are implicated in genome stability rather than in generating adaptive variation. DUS elements are most frequent in the permissive locations of the core genome but are themselves highly conserved, undergoing mutation selection balance and/or molecular drive. Similar preliminary results were found for the functionally analogous uptake signal sequence in Pasteurellaceae. Conclusion As do many other pathogens, Neisseria and Pasteurellaceae have hyperdynamic genomes that generate deleterious mutations by intrachromosomal recombination and by transient hypermutation. The results presented here suggest that transformation in Neisseria and Pasteurellaceae allows them to counteract the deleterious effects of genome instability in the core genome. Thus, rather than promoting hypervariation, bacterial sex could be regenerative. PMID:18366792

  14. Type III polyketide synthase repertoire in Zingiberaceae: computational insights into the sequence, structure and evolution.

    PubMed

    Mallika, Vijayanathan; Aiswarya, Girija; Gincy, Paily Thottathil; Remakanthan, Appukuttan; Soniya, Eppurathu Vasudevan

    2016-07-01

    Zingiberaceae or 'ginger family' is the largest family in the order 'Zingiberales' with more than 1300 species in 52 genera, which are mostly distributed throughout Asia, tropical Africa and the native regions of America with their maximum diversity in Southeast Asia. Many of the members are important spice, medicinal or ornamental plants including ginger, turmeric, cardamom and kaempferia. These plants are distinguished for the highly valuable metabolic products, which are synthesised through phenylpropanoid pathway, where type III polyketide synthase is the key enzyme. In our present study, we used sequence, structural and evolutionary approaches to scrutinise the type III polyketide synthase (PKS) repertoire encoded in the Zingiberaceae family. Highly conserved amino acid residues in the sequence alignment and phylogram suggested strong relationships between the type III PKS members of Zingiberaceae. Sequence and structural level investigation of type III PKSs showed a small number of variations in the substrate binding pocket, leading to functional divergence among these PKS members. Molecular evolutionary studies indicate that type III PKSs within Zingiberaceae evolved under strong purifying selection pressure, and positive selections were rarely detected in the family. Structural modelling and protein-small molecule interaction studies on Zingiber officinale PKS 'a representative from Zingiberaceae' suggested that the protein is comparatively stable without much disorder and exhibited wide substrate acceptance. PMID:27138283

  15. Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information.

    PubMed

    Wang, Kai; Horst, Jeremy A; Cheng, Gong; Nickle, David C; Samudrala, Ram

    2008-09-26

    Protein function is mediated by different amino acid residues, both their positions and types, in a protein sequence. Some amino acids are responsible for the stability or overall shape of the protein, playing an indirect role in protein function. Others play a functionally important role as part of active or binding sites of the protein. For a given protein sequence, the residues and their degree of functional importance can be thought of as a signature representing the function of the protein. We have developed a combination of knowledge- and biophysics-based function prediction approaches to elucidate the relationships between the structural and the functional roles of individual residues and positions. Such a meta-functional signature (MFS), which is a collection of continuous values representing the functional significance of each residue in a protein, may be used to study proteins of known function in greater detail and to aid in experimental characterization of proteins of unknown function. We demonstrate the superior performance of MFS in predicting protein functional sites and also present four real-world examples to apply MFS in a wide range of settings to elucidate protein sequence-structure-function relationships. Our results indicate that the MFS approach, which can combine multiple sources of information and also give biological interpretation to each component, greatly facilitates the understanding and characterization of protein function.

  16. Sequence co-evolution gives 3D contacts and structures of protein complexes

    PubMed Central

    Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

    2014-01-01

    Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

  17. Sequence evolution in and around the mitochondrial control region in birds.

    PubMed

    Quinn, T W; Wilson, A C

    1993-10-01

    By cloning and sequencing 3.4 kilobases of snow goose mtDNA we found that the ND5 gene is followed by the genes for cytochrome b, tRNA(Thr), tRNA(Pro), ND6, tRNA(Glu), the control region, tRNA(Phe), and srRNA. This order is identical to that of chicken, quail, and duck mtDNA but differs from that of mammals and a frog (Xenopus). The mean extent of difference due to base substitution between goose and chicken is generally closer to the same comparison between rat and mouse but less than that between human and cow. For one of the nine regions compared (tRNA(Glu)), the bird differences appear to be anomalous, possibly implicating altered functional constraints. Within the control region, several short sequences common to mammals are also conserved in the birds. Comparison of the goose control region with that of quail and chicken suggests that a sequence element with similarity to CSB-1 duplicated once prior to the divergence of goose and chicken and again on the lineage leading to chicken. Between goose (or duck) and chicken there are four times more transversions at the third positions of fourfold-degenerate codons in mitochondrial than in nuclear genes. PMID:8308909

  18. Late Neogene Sequence Stratigraphic Evolution of the Foz do Amazonas Basin, Brazil

    NASA Astrophysics Data System (ADS)

    Gorini, Christian; Haq, Bilal U.; Tadeu dos Reis, Antonio; Guizan Silva, Cleverson; Cruz, Alberto; Soares, Emilson; Grangeon, Didier

    2014-05-01

    The margin of the Foz do Amazonas Basin saw a shift from predominantly carbonate to siliciclastic sedimentation in the early late Miocene. By this time the Amazon shelf had also been incised by a canyon that allowed direct influx of sediment to the basin floor, thus confirming that the paleo-Amazon fan had already initiated by that time (9.5-8.3Ma). Above this interval, during a prolonged lowstand, Messinian third-order sequences are preserved only in the incised-valley fills of the canyon with no equivalent strata on the shelf. Third and fourth-order sequences younger than Messinian are preserved on the shelf after sea-level rise above the shelf by early Pliocene. Sequences younger than 3.8 Ma often show fourth-order cyclicity with average duration of 400 kyr (larger scale eccentricity cycles) often preserved in high sedimentation rate areas of river deltas. Mass wasting and transportation of slope sediments to the basin began to play an important role in sediment dispersal at least as far back as mid Pliocene, after rapid progradation had produced steeper slopes 23 more prone to failure.

  19. The white-dwarf cooling sequence of NGC 6791: a unique tool for stellar evolution

    NASA Astrophysics Data System (ADS)

    García-Berro, E.; Torres, S.; Renedo, I.; Camacho, J.; Althaus, L. G.; Córsico, A. H.; Salaris, M.; Isern, J.

    2011-09-01

    Context. NGC 6791 is a well-studied, metal-rich open cluster that is so close to us that it can be imaged down to luminosities fainter than that of the termination of its white-dwarf cooling sequence, thus allowing for an in-depth study of its white dwarf population. Aims: White dwarfs carry important information about the history of the cluster. We use observations of the white-dwarf cooling sequence to constrain important properties of the cluster stellar population, such as the existence of a putative population of massive helium-core white dwarfs, and the properties of a large population of unresolved binary white dwarfs. We also investigate the use of white dwarfs to disclose the presence of cluster subpopulations with a different initial chemical composition, and we obtain an upper bound to the fraction of hydrogen-deficient white dwarfs. Methods: We use a Monte Carlo simulator that employs up-to-date evolutionary cooling sequences for white dwarfs with hydrogen-rich and hydrogen-deficient atmospheres, with carbon-oxygen and helium cores. The cooling sequences for carbon-oxygen cores account for the delays introduced by both 22Ne sedimentation in the liquid phase and by carbon-oxygen phase separation upon crystallization. Results: We do not find evidence for a substantial fraction of helium-core white dwarfs, and hence our results support the suggestion that the origin of the bright peak of the white-dwarf luminosity function can only be attributed to a population of unresolved binary white dwarfs. Moreover, our results indicate that if this hypothesis is at the origin of the bright peak, the number distribution of secondary masses of the population of unresolved binaries has to increase with increasing mass ratio between the secondary and primary components of the progenitor system. We also find that the observed cooling sequence appears to be able to constrain the presence of progenitor subpopulations with different chemical compositions and the fraction of

  20. Evolution of Mhc Class i Complex Region with Special Reference to Fragmentary Line Sequences

    NASA Astrophysics Data System (ADS)

    Tateno, Yoshio; Fukami-Kobayashi, Kaoru; Inoko, Hidetoshi

    2008-03-01

    We reviewed the origin and evolution of the two pairs of immune genes, (MHC-B and MHC-C) and (MICA and MICB) in man, chimpanzee and rhesus monkey based mainly on our previous work. Since those genes were well known to have been subject to strong natural selection in evolution, they themselves were not suitable for our study. We thus took another approach to use fragmented and nonfunctional LINEs that had coevolved with the two pairs in the same genomic fragments. Our results showed that MHC-B and MHC-C duplicated about 22 Mry (million years) ago, and MICA and MICB duplicated about 14 Myr ago. Interestingly, rhesus monkey was found not to have either pair but many repeats similar to MHC-B. Therefore, we estimated the divergence time of the monkey, and found that it diverged out from a common ancestor of man and chimpanzee about 30 Myr ago. The divergence time was consistent with the duplication times of the two pairs of immune genes. Based on our results we would predict that orangutan and gorilla also have the two pairs, because the both primate species are considered to have diverged less than 14 Myr ago.

  1. Accelerating Gene Discovery by Phenotyping Whole-Genome Sequenced Multi-mutation Strains and Using the Sequence Kernel Association Test (SKAT).

    PubMed

    Timbers, Tiffany A; Garland, Stephanie J; Mohan, Swetha; Flibotte, Stephane; Edgley, Mark; Muncaster, Quintin; Au, Vinci; Li-Leger, Erica; Rosell, Federico I; Cai, Jerry; Rademakers, Suzanne; Jansen, Gert; Moerman, Donald G; Leroux, Michel R

    2016-08-01

    Forward genetic screens represent powerful, unbiased approaches to uncover novel components in any biological process. Such screens suffer from a major bottleneck, however, namely the cloning of corresponding genes causing the phenotypic variation. Reverse genetic screens have been employed as a way to circumvent this issue, but can often be limited in scope. Here we demonstrate an innovative approach to gene discovery. Using C. elegans as a model system, we used a whole-genome sequenced multi-mutation library, from the Million Mutation Project, together with the Sequence Kernel Association Test (SKAT), to rapidly screen for and identify genes associated with a phenotype of interest, namely defects in dye-filling of ciliated sensory neurons. Such anomalies in dye-filling are often associated with the disruption of cilia, organelles which in humans are implicated in sensory physiology (including vision, smell and hearing), development and disease. Beyond identifying several well characterised dye-filling genes, our approach uncovered three genes not previously linked to ciliated sensory neuron development or function. From these putative novel dye-filling genes, we confirmed the involvement of BGNT-1.1 in ciliated sensory neuron function and morphogenesis. BGNT-1.1 functions at the trans-Golgi network of sheath cells (glia) to influence dye-filling and cilium length, in a cell non-autonomous manner. Notably, BGNT-1.1 is the orthologue of human B3GNT1/B4GAT1, a glycosyltransferase associated with Walker-Warburg syndrome (WWS). WWS is a multigenic disorder characterised by muscular dystrophy as well as brain and eye anomalies. Together, our work unveils an effective and innovative approach to gene discovery, and provides the first evidence that B3GNT1-associated Walker-Warburg syndrome may be considered a ciliopathy. PMID:27508411

  2. Accelerating Gene Discovery by Phenotyping Whole-Genome Sequenced Multi-mutation Strains and Using the Sequence Kernel Association Test (SKAT)

    PubMed Central

    Garland, Stephanie J.; Mohan, Swetha; Flibotte, Stephane; Muncaster, Quintin; Cai, Jerry; Rademakers, Suzanne; Moerman, Donald G.; Leroux, Michel R.

    2016-01-01

    Forward genetic screens represent powerful, unbiased approaches to uncover novel components in any biological process. Such screens suffer from a major bottleneck, however, namely the cloning of corresponding genes causing the phenotypic variation. Reverse genetic screens have been employed as a way to circumvent this issue, but can often be limited in scope. Here we demonstrate an innovative approach to gene discovery. Using C. elegans as a model system, we used a whole-genome sequenced multi-mutation library, from the Million Mutation Project, together with the Sequence Kernel Association Test (SKAT), to rapidly screen for and identify genes associated with a phenotype of interest, namely defects in dye-filling of ciliated sensory neurons. Such anomalies in dye-filling are often associated with the disruption of cilia, organelles which in humans are implicated in sensory physiology (including vision, smell and hearing), development and disease. Beyond identifying several well characterised dye-filling genes, our approach uncovered three genes not previously linked to ciliated sensory neuron development or function. From these putative novel dye-filling genes, we confirmed the involvement of BGNT-1.1 in ciliated sensory neuron function and morphogenesis. BGNT-1.1 functions at the trans-Golgi network of sheath cells (glia) to influence dye-filling and cilium length, in a cell non-autonomous manner. Notably, BGNT-1.1 is the orthologue of human B3GNT1/B4GAT1, a glycosyltransferase associated with Walker-Warburg syndrome (WWS). WWS is a multigenic disorder characterised by muscular dystrophy as well as brain and eye anomalies. Together, our work unveils an effective and innovative approach to gene discovery, and provides the first evidence that B3GNT1-associated Walker-Warburg syndrome may be considered a ciliopathy. PMID:27508411

  3. Repetitive DNA Sequences and Evolution of ZZ/ZW Sex Chromosomes in Characidium (Teleostei: Characiformes)

    PubMed Central

    Pansonato-Alves, José Carlos; da Costa Silva, Guilherme José; Vicari, Marcelo Ricardo; Artoni, Roberto Ferreira; Oliveira, Claudio; Foresti, Fausto

    2015-01-01

    Characidium constitutes an interesting model for cytogenetic studies, since a large degree of karyotype variation has been detected in this group, like the presence/absence of sex and supernumerary chromosomes and variable distribution of repetitive sequences in different species/populations. In this study, we performed a comparative cytogenetic analysis in 13 Characidium species collected at different South American river basins in order to investigate the karyotype diversification in this group. Chromosome analyses involved the karyotype characterization, cytogenetic mapping of repetitive DNA sequences and cross-species chromosome painting using a W-specific probe obtained in a previous study from Characidium gomesi. Our results evidenced a conserved diploid chromosome number of 2n = 50, and almost all the species exhibited homeologous ZZ/ZW sex chromosomes in different stages of differentiation, except C. cf. zebra, C. tenue, C. xavante and C. stigmosum. Notably, some ZZ/ZW sex chromosomes showed 5S and/or 18S rDNA clusters, while no U2 snDNA sites could be detected in the sex chromosomes, being restricted to a single chromosome pair in almost all the analyzed species. In addition, the species Characidium sp. aff. C. vidali showed B chromosomes with an inter-individual variation of 1 to 4 supernumerary chromosomes per cell. Notably, these B chromosomes share sequences with the W-specific probe, providing insights about their origin. Results presented here further confirm the extensive karyotype diversity within Characidium in contrast with a conserved diploid chromosome number. Such chromosome differences seem to constitute a significant reproductive barrier, since several sympatric Characidium species had been described during the last few years and no interespecific hybrids were found. PMID:26372604

  4. Hydration sequence of swelling clays: evolutions of specific surface area and hydration energy.

    PubMed

    Salles, Fabrice; Douillard, Jean-Marc; Denoyel, Renaud; Bildstein, Olivier; Jullien, Michel; Beurroies, Isabelle; Van Damme, Henri

    2009-05-15

    In order to identify the key steps and the driving force for the hydration process of swelling clays, the water adsorption isotherms and enthalpies were measured on monoionic montmorillonite samples saturated with alkali or calcium ions, and on bi-ionic samples saturated with a sodium-calcium mixture. The specific surface area evolution along the hydration process was determined using a recent interpretation of the experimental adsorption isotherms of swelling solids. Results are interpreted in structural terms. Compared with additional data from sample-controlled thermal analysis (SCTA), the results confirm experimentally that the hydration of Li- and Na-montmorillonite is mainly a cation-controlled process, in contrast with the hydration of Cs samples in which the cation contribution to hydration is negligible, as we have already demonstrated using electrostatic calculations or conductivity measurements. PMID:19303602

  5. The Rho GTPase Family Genes in Bivalvia Genomes: Sequence, Evolution and Expression Analysis

    PubMed Central

    Li, Xue; Wang, Ruijia; Xun, Xiaogang; Jiao, Wenqian; Zhang, Mengran; Wang, Shuyue; Wang, Shi; Zhang, Lingling; Huang, Xiaoting; Hu, Xiaoli; Bao, Zhenmin

    2015-01-01

    Background Rho GTPases are important members of the Ras superfamily, which represents the largest signaling protein family in eukaryotes, and function as key molecular switches in converting and amplifying external signals into cellular responses. Although numerous analyses of Rho family genes have been reported, including their functions and evolution, a systematic analysis of this family has not been performed in Mollusca or in Bivalvia, one of the most important classes of Mollusca. Results In this study, we systematically identified and characterized a total set (Rho, Rac, Mig, Cdc42, Tc10, Rnd, RhoU, RhoBTB and Miro) of thirty Rho GTPase genes in three bivalve species, including nine in the Yesso scallop Patinopecten yessoensis, nine in the Zhikong scallop Chlamys farreri, and twelve in the Pacific oyster Crassostrea gigas. Phylogenetic analysis and interspecies comparison indicated that bivalves might possess the most complete types of Rho genes in invertebrates. A multiple RNA-seq dataset was used to investigate the expression profiles of bivalve Rho genes, revealing that the examined scallops share more similar Rho expression patterns than the oyster, whereas more Rho mRNAs are expressed in C. farreri and C. gigas than in P. yessoensis. Additionally, Rho, Rac and Cdc42 were found to be duplicated in the oyster but not in the scallops. Among the expanded Rho genes of C. gigas, duplication pairs with high synonymous substitution rates (Ks) displayed greater differences in expression. Conclusion A comprehensive analysis of bivalve Rho GTPase family genes was performed in scallop and oyster species, and Rho genes in bivalves exhibit greater conservation than those in any other invertebrate. This is the first study focusing on a genome-wide characterization of Rho GTPase genes in bivalves, and the findings will provide a valuable resource for a better understanding of Rho evolution and Rho GTPase function in Bivalvia. PMID:26633655

  6. Mouse annexin V chromosomal localization, cDNA sequence conservation, and molecular evolution

    SciTech Connect

    Rodriguez-Garcia, M.I.; Morgan, R.O.; Kozak, C.A.

    1996-01-15

    A full-length cDNA encoding mouse annexin V (ANX5) was cloned, sequenced, and utilized for chromosomal mapping. The gene lies on mouse chromosome 3 in close linkage with the fibroblast growth factor 2 (basic) gene and is syntenic with other genes known to have orthologous counterparts on human chromosome 4q. The open reading frame encoded a protein of 319 amino acids (aa), with 92-96% identity to ANX5 in other species. Internal repeat 3 of mouse ANX5 exhibited the highest level of nonconservative aa replacements with respect to other annexin subfamilies, but the greatest sequence conservation among ANX5 species members. This region may thus contain features that distinguish ANX5 from other annexins in properties or function. Phylogenetic analysis and homology testing of ANX5 members indicated that the 34-kDa annexin from Torpedo marmorata may also belong to this subfamily. Comparison of nine species of ANX5 led to an estimation of the unit evolutionary mutation rate at 1% aa replacements every 8 million years, comparable to other annexins. 46 refs., 4 figs.

  7. Evolution of satellite DNA sequences in two tribes of Bovidae: A cautionary tale.

    PubMed

    Nieddu, Mariella; Mezzanotte, Roberto; Pichiri, Giuseppina; Coni, Pier Paolo; Dedola, Gian Luca; Dettori, Maria Luisa; Pazzola, Michele; Vacca, Giuseppe Massimo; Robledo, Renato

    2015-12-01

    Two clones, Bt1 from Bos taurus and Om1 from Ovis orientalis musimon, were used as probes for hybridization on genomic DNA and on metaphase chromosomes in members of Bovini and Caprini tribes. Bt1 and Om1 are sequences respectively belonging to the 1.715 and 1.714 DNA satellite I families. Southern blots and fluorescence in situ hybridization experiments showed completely coherent results: the Bovini probe Bt1 hybridized only to members of the Bovini tribe and not to members of Caprini. Likewise, the Caprini probe Om1 hybridized only to members of the Caprini tribe and not to members of Bovini. Hybridization signals were detected in the heterochromatic regions of every acrocentric autosome, except for two pairs of autosomes from Capra hircus that did not show hybridization to probe Om1. No signal was detected on X and Y chromosomes or on bi-armed autosomes. Remarkably, probe Om1 showed almost 100% homology with a bacterial sequence reported in Helicobacter pylori. PMID:26692159

  8. Genomic and polyploid evolution in genus Avena as revealed by RFLPs of repeated DNA sequences.

    PubMed

    Morikawa, Toshinobu; Nishihara, Miho

    2009-06-01

    Phylogenetic relationships and genome affinities were investigated by utilizing all the biological Avena species consisting of 11 diploid species (15 accessions), 8 tetraploid species (9 accessions) and 4 hexaploid species (5 accessions). Genomic DNA regions of As120a, avenin, and globulin were amplified by PCR. A total of 130 polymorphic fragments were detected out of 156 fragments generated by digesting the PCR-amplified fragments with 11 restriction enzymes. The number of fragments generated by PCR-amplification followed by digestion with restriction enzymes was almost the same as those among the three repeated DNA sequences. A high level of genetic distance was detected between A. damascena (Ad) and A. canariensis (Ac) genomes, which reflected their different morphology and reproductive isolation. The A. longiglumis (Al) and A. prostrata (Ap) genomes were closely related to the As genome group. The AB genome species formed a cluster with the AsAs genome artificial autotetraploid and the As genome diploids indicating near-autotetraploid origin. The A. macrostachya is an outbreeding autotetraploid closely related with the C genome diploid and the AC genome tetraploid species. The differences of genetic distances estimated from the repeated DNA sequence divergence among the Avena species were consistent with genome divergences and it was possible to compare the genetic intra- and inter-ploidy relationships produced by RFLPs. These results suggested that the PCR-mediated analysis of repeated DNA polymorphism can be used as a tool to examine genomic relationships of polyploidy species.

  9. Evolution of satellite DNA sequences in two tribes of Bovidae: A cautionary tale

    PubMed Central

    Nieddu, Mariella; Mezzanotte, Roberto; Pichiri, Giuseppina; Coni, Pier Paolo; Dedola, Gian Luca; Dettori, Maria Luisa; Pazzola, Michele; Vacca, Giuseppe Massimo; Robledo, Renato

    2015-01-01

    Abstract Two clones, Bt1 from Bos taurus and Om1 from Ovis orientalis musimon, were used as probes for hybridization on genomic DNA and on metaphase chromosomes in members of Bovini and Caprini tribes. Bt1 and Om1 are sequences respectively belonging to the 1.715 and 1.714 DNA satellite I families. Southern blots and fluorescence in situ hybridization experiments showed completely coherent results: the Bovini probe Bt1 hybridized only to members of the Bovini tribe and not to members of Caprini. Likewise, the Caprini probe Om1 hybridized only to members of the Caprini tribe and not to members of Bovini. Hybridization signals were detected in the heterochromatic regions of every acrocentric autosome, except for two pairs of autosomes from Capra hircus that did not show hybridization to probe Om1. No signal was detected on X and Y chromosomes or on bi-armed autosomes. Remarkably, probe Om1 showed almost 100% homology with a bacterial sequence reported in Helicobacter pylori. PMID:26692159

  10. Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation.

    PubMed

    Schlötterer, C; Kofler, R; Versace, E; Tobler, R; Franssen, S U

    2015-05-01

    Evolve and resequence (E&R) is a new approach to investigate the genomic responses to selection during experimental evolution. By using whole genome sequencing of pools of individuals (Pool-Seq), this method can identify selected variants in controlled and replicable experimental settings. Reviewing the current state of the field, we show that E&R can be powerful enough to identify causative genes and possibly even single-nucleotide polymorphisms. We also discuss how the experimental design and the complexity of the trait could result in a large number of false positive candidates. We suggest experimental and analytical strategies to maximize the power of E&R to uncover the genotype-phenotype link and serve as an important research tool for a broad range of evolutionary questions.

  11. Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients

    PubMed Central

    Merker, Matthias; Kohl, Thomas A.; Roetzer, Andreas; Truebe, Leona; Richter, Elvira; Rüsch-Gerdes, Sabine; Fattorini, Lanfranco; Oggioni, Marco R.; Cox, Helen; Varaine, Francis; Niemann, Stefan

    2013-01-01

    Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains represent a major threat for tuberculosis (TB) control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR) variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS) to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A) and nine (Patient B) polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and molecular drug

  12. Evolution of the single-mode Rayleigh-Taylor instability under the influence of time-dependent accelerations.

    PubMed

    Ramaprabhu, P; Karkhanis, V; Banerjee, R; Varshochi, H; Khan, M; Lawrie, A G W

    2016-01-01

    From nonlinear models and direct numerical simulations we report on several findings of relevance to the single-mode Rayleigh-Taylor (RT) instability driven by time-varying acceleration histories. The incompressible, direct numerical simulations (DNSs) were performed in two (2D) and three dimensions (3D), and at a range of density ratios of the fluid combinations (characterized by the Atwood number). We investigated several acceleration histories, including acceleration profiles of the general form g(t)∼t^{n}, with n≥0 and acceleration histories reminiscent of the linear electric motor experiments. For the 2D flow, results from numerical simulations compare well with a 2D potential flow model and solutions to a drag-buoyancy model reported as part of this work. When the simulations are extended to three dimensions, bubble and spike growth rates are in agreement with the so-called level 2 and level 3 models of Mikaelian [K. O. Mikaelian, Phys. Rev. E 79, 065303(R) (2009)10.1103/PhysRevE.79.065303], and with corresponding 3D drag-buoyancy model solutions derived in this article. Our generalization of the RT problem to study variable g(t) affords us the opportunity to investigate the appropriate scaling for bubble and spike amplitudes under these conditions. We consider two candidates, the displacement Z and width s^{2}, but find the appropriate scaling is dependent on the density ratios between the fluids-at low density ratios, bubble and spike amplitudes are explained by both s^{2} and Z, while at large density differences the displacement collapses the spike data. Finally, for all the acceleration profiles studied here, spikes enter a free-fall regime at lower Atwood numbers than predicted by all the models. PMID:26871165

  13. Evolution of the single-mode Rayleigh-Taylor instability under the influence of time-dependent accelerations

    NASA Astrophysics Data System (ADS)

    Ramaprabhu, P.; Karkhanis, V.; Banerjee, R.; Varshochi, H.; Khan, M.; Lawrie, A. G. W.

    2016-01-01

    From nonlinear models and direct numerical simulations we report on several findings of relevance to the single-mode Rayleigh-Taylor (RT) instability driven by time-varying acceleration histories. The incompressible, direct numerical simulations (DNSs) were performed in two (2D) and three dimensions (3D), and at a range of density ratios of the fluid combinations (characterized by the Atwood number). We investigated several acceleration histories, including acceleration profiles of the general form g (t ) ˜tn , with n ≥0 and acceleration histories reminiscent of the linear electric motor experiments. For the 2D flow, results from numerical simulations compare well with a 2D potential flow model and solutions to a drag-buoyancy model reported as part of this work. When the simulations are extended to three dimensions, bubble and spike growth rates are in agreement with the so-called level 2 and level 3 models of Mikaelian [K. O. Mikaelian, Phys. Rev. E 79, 065303(R) (2009), 10.1103/PhysRevE.79.065303], and with corresponding 3D drag-buoyancy model solutions derived in this article. Our generalization of the RT problem to study variable g (t ) affords us the opportunity to investigate the appropriate scaling for bubble and spike amplitudes under these conditions. We consider two candidates, the displacement Z and width s2, but find the appropriate scaling is dependent on the density ratios between the fluids—at low density ratios, bubble and spike amplitudes are explained by both s2 and Z , while at large density differences the displacement collapses the spike data. Finally, for all the acceleration profiles studied here, spikes enter a free-fall regime at lower Atwood numbers than predicted by all the models.

  14. Evolution of the single-mode Rayleigh-Taylor instability under the influence of time-dependent accelerations.

    PubMed

    Ramaprabhu, P; Karkhanis, V; Banerjee, R; Varshochi, H; Khan, M; Lawrie, A G W

    2016-01-01

    From nonlinear models and direct numerical simulations we report on several findings of relevance to the single-mode Rayleigh-Taylor (RT) instability driven by time-varying acceleration histories. The incompressible, direct numerical simulations (DNSs) were performed in two (2D) and three dimensions (3D), and at a range of density ratios of the fluid combinations (characterized by the Atwood number). We investigated several acceleration histories, including acceleration profiles of the general form g(t)∼t^{n}, with n≥0 and acceleration histories reminiscent of the linear electric motor experiments. For the 2D flow, results from numerical simulations compare well with a 2D potential flow model and solutions to a drag-buoyancy model reported as part of this work. When the simulations are extended to three dimensions, bubble and spike growth rates are in agreement with the so-called level 2 and level 3 models of Mikaelian [K. O. Mikaelian, Phys. Rev. E 79, 065303(R) (2009)10.1103/PhysRevE.79.065303], and with corresponding 3D drag-buoyancy model solutions derived in this article. Our generalization of the RT problem to study variable g(t) affords us the opportunity to investigate the appropriate scaling for bubble and spike amplitudes under these conditions. We consider two candidates, the displacement Z and width s^{2}, but find the appropriate scaling is dependent on the density ratios between the fluids-at low density ratios, bubble and spike amplitudes are explained by both s^{2} and Z, while at large density differences the displacement collapses the spike data. Finally, for all the acceleration profiles studied here, spikes enter a free-fall regime at lower Atwood numbers than predicted by all the models.

  15. Phylogeny, hybridization, and life history evolution of Rhinogobius gobies in Japan, inferred from multiple nuclear gene sequences.

    PubMed

    Yamasaki, Yo Y; Nishida, Mutsumi; Suzuki, Toshiyuki; Mukai, Takahiko; Watanabe, Katsutoshi

    2015-09-01

    Rhinogobius fishes (Gobiidae) are distributed widely in East and Southeast Asia, and represent the most species-rich group of freshwater gobies with diversified life histories (i.e., amphidromous, fluvial, and lentic). To reveal their phylogenetic relationships and life history evolution patterns, we sequenced six nuclear and three mitochondrial DNA (mtDNA) loci from 18 species, mainly from the mainland of Japan and the Ryukyu Archipelago. Our phylogenetic tree based on nuclear genes resolved three major clades, including several distinct subclades. The mtDNA and nuclear DNA phylogenies showed large discordance, which strongly suggested mitochondrial introgression through large-scale interspecific hybridization in these regions. On the basis of the molecular dating using geological data as calibration points, the hybridization occurred in the early to middle Pleistocene. Reconstruction of the ancestral states of life history traits based on nuclear DNA phylogeny suggests that the evolutionary change from amphidromous to freshwater life, accompanied by egg size change, occurred independently in at least three lineages. One of these lineages showed two life history alterations, i.e., from amphidromous (small egg) to fluvial (large egg) to lentic (small egg). Although more inclusive analysis using species outside Japan should be further conducted, the present results suggest the importance of the life history evolution associated with high adaptability to freshwater environments in the remarkable species diversification in this group. Such life history divergences may have contributed to the development of reproductive isolation.

  16. Phylogeny, hybridization, and life history evolution of Rhinogobius gobies in Japan, inferred from multiple nuclear gene sequences.

    PubMed

    Yamasaki, Yo Y; Nishida, Mutsumi; Suzuki, Toshiyuki; Mukai, Takahiko; Watanabe, Katsutoshi

    2015-09-01

    Rhinogobius fishes (Gobiidae) are distributed widely in East and Southeast Asia, and represent the most species-rich group of freshwater gobies with diversified life histories (i.e., amphidromous, fluvial, and lentic). To reveal their phylogenetic relationships and life history evolution patterns, we sequenced six nuclear and three mitochondrial DNA (mtDNA) loci from 18 species, mainly from the mainland of Japan and the Ryukyu Archipelago. Our phylogenetic tree based on nuclear genes resolved three major clades, including several distinct subclades. The mtDNA and nuclear DNA phylogenies showed large discordance, which strongly suggested mitochondrial introgression through large-scale interspecific hybridization in these regions. On the basis of the molecular dating using geological data as calibration points, the hybridization occurred in the early to middle Pleistocene. Reconstruction of the ancestral states of life history traits based on nuclear DNA phylogeny suggests that the evolutionary change from amphidromous to freshwater life, accompanied by egg size change, occurred independently in at least three lineages. One of these lineages showed two life history alterations, i.e., from amphidromous (small egg) to fluvial (large egg) to lentic (small egg). Although more inclusive analysis using species outside Japan should be further conducted, the present results suggest the importance of the life history evolution associated with high adaptability to freshwater environments in the remarkable species diversification in this group. Such life history divergences may have contributed to the development of reproductive isolation. PMID:25929788

  17. Evolution of the rhodospirillaceae and mitochondria - A view based on sequence data

    NASA Technical Reports Server (NTRS)

    Dayhoff, M. O.; Schwartz, R. M.

    1981-01-01

    New sequence data from several protein families and from 5S ribosomal RNA confirm and elaborate a previously proposed description of the phylogenetic connections between a variety of bacteria and the eukaryotes. Probably, the first organisms were nonphotosynthetic anaerobic prokaryotes, which were followed soon by photosynthetic anaerobes. From this photosynthetic stock, the aerobic line to Pseudomonadacae, Rhodospirillaceae, and blue-greens arose. The eukaryotes derived genetic material from the symbioses of at least three separate bacterial lines. Ancestors of Rhodopseudomonas globiformis gave rise to the eukaryote mitochondria, probably through at least three separate symbioses, one early on the flagellate line, one on the ciliate line, and one on the stem to the multicellular forms.

  18. Beyond Junk-Variable Tandem Repeats as Facilitators of Rapid Evolution of Regulatory and Coding Sequences

    PubMed Central

    Gemayel, Rita; Cho, Janice; Boeynaems, Steven; Verstrepen, Kevin J.

    2012-01-01

    Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms (SNPs) have been the major focus of most large-scale comparative genomics studies to date. Here, we discuss a third, largely ignored, type of genetic variation, namely changes in tandem repeat number. Historically, tandem repeats have been designated as non functional “junk” DNA, mostly as a result of their highly unstable nature. With the exception of tandem repeats involved in human neurodegenerative diseases, repeat variation was often believed to be neutral with no phenotypic consequences. Recent studies, however, have shown that as many as 10% to 20% of coding and regulatory sequences in eukaryotes contain an unstable repeat tract. Contrary to initial suggestions, tandem repeat variation can have useful phenotypic consequences. Examples include rapid variation in microbial cell surface, tuning of internal molecular clocks in flies and the dynamic morphological plasticity in mammals. As such, tandem repeats can be useful functional elements that facilitate evolvability and rapid adaptation. PMID:24704980

  19. Evolution of early life inferred from protein and ribonucleic acid sequences

    NASA Technical Reports Server (NTRS)

    Dayhoff, M. O.; Schwartz, R. M.

    1978-01-01

    The chemical structures of ferredoxin, 5S ribosomal RNA, and c-type cytochrome sequences have been employed to construct a phylogenetic tree which connects all major photosynthesizing organisms: the three types of bacteria, blue-green algae, and chloroplasts. Anaerobic and aerobic bacteria, eukaryotic cytoplasmic components and mitochondria are also included in the phylogenetic tree. Anaerobic nonphotosynthesizing bacteria similar to Clostridium were the earliest organisms, arising more than 3.2 billion years ago. Bacterial photosynthesis evolved nearly 3.0 billion years ago, while oxygen-evolving photosynthesis, originating in the blue-green algal line, came into being about 2.0 billion years ago. The phylogenetic tree supports the symbiotic theory of the origin of eukaryotes.

  20. Sequence stratigraphy as a scientific enterprise: the evolution and persistence of conflicting paradigms

    NASA Astrophysics Data System (ADS)

    Miall, Andrew D.; Miall, Charlene E.

    2001-08-01

    In the 1970s, seismic stratigraphy represented a new paradigm in geological thought. The development of new techniques for analyzing seismic-reflection data constituted a "crisis," as conceptualized by T.S. Kuhn, and stimulated a revolution in stratigraphy. We analyze here a specific subset of the new ideas, that pertaining to the concept of global-eustasy and the global cycle chart published by Vail et al. [Vail, P.R., Mitchum, R.M., Jr., Todd, R.G., Widmier, J.M., Thompson, S., III, Sangree, J.B., Bubb, J.N., Hatlelid, W.G., 1977. Seismic stratigraphy and global changes of sea-level. In: Payton, C.E. (Ed.), Seismic Stratigraphy—Applications to Hydrocarbon Exploration, Am. Assoc. Pet. Geol. Mem. 26, pp. 49-212.] The global-eustasy model posed two challenges to the "normal science" of stratigraphy then underway: (1) that sequence stratigraphy, as exemplified by the global cycle chart, constitutes a superior standard of geologic time to that assembled from conventional chronostratigraphic evidence, and (2) that stratigraphic processes are dominated by the effects of eustasy, to the exclusion of other allogenic mechanisms, including tectonism. While many stratigraphers now doubt the universal validity of the model of global-eustasy, what we term the global-eustasy paradigm, a group of sequence researchers led by Vail still adheres to it, and the two conceptual approaches have evolved into two conflicting paradigms. Those who assert that there are multiple processes generating stratigraphic sequences (possibly including eustatic processes) are adherents of what we term the complexity paradigm. Followers of this paradigm argue that tests of the global cycle chart amount to little more than circular reasoning. A new body of work documenting the European sequence record was published in 1998 by de Graciansky et al. These workers largely follow the global-eustasy paradigm. Citation and textual analysis of this work indicates that they have not responded to any of the

  1. Stratigraphic evolution of Mesozoic continental margin and oceanic sequences northwest Australia and north Himalayas

    SciTech Connect

    Gradstein, F.M. ); Von Rad, U. )

    1990-05-01

    The authors are investigating continental margin to ocean sequences of the incipient Indian Ocean as it replaced central Tethys. Objectives of this study are the dynamic relation between sedimentation, tectonics, and paleogeography. Principal basins formation along the northern edge of eastern Gondwana started in the Late Permian to the Triassic. By the Late Triassic-Early Jurassic, platform carbonates with thin, organic-rich lagoonal shales were laid down in a subtropical climate. This unit, which harbors some of the oldest known nannofossils, shows repeated shallowing-upward sequences. Subsequent southward drift of the Gondwana margin during the Middle Jurassic increased siliciclastic input in Nepal, when widespread sediment starvation or erosion during local uplift took place off parts of northwest Australia. A middle Callovian-early Oxfordian hiatus in Nepal is submarine and appears global in extent. The overlying 250-m-thick organic-rich black shales, correlative to the Oxford/Kimmeridge clays of circum-Atlantic petroleum basins, may be traced along