The Impact of the Brazos Deltaic System on Upper Slope Stratigraphic Sequence Evolution

2003 ◽  
pp. 325-357 ◽  
Author(s):  
Carmen M. Fraticelli ◽  
John B. Anderson
Keyword(s):  
Sequence Evolution ◽  
Stratigraphic Sequence ◽  
The Impact ◽  
Upper Slope

scholarly journals The impact of epigenetic information on genome evolution

2021 ◽  
Vol 376 (1826) ◽  
Author(s):  
Soojin V. Yi ◽  
Michael A. D. Goodisman
Keyword(s):  
Genome Evolution ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Evolution ◽  
Epigenetic Information ◽  
Dna Mutation ◽  
Dna Mutations ◽  
Physical Interactions ◽  
Eukaryotic Organisms ◽  
The Impact

Epigenetic information affects gene function by interacting with chromatin, while not changing the DNA sequence itself. However, it has become apparent that the interactions between epigenetic information and chromatin can, in fact, indirectly lead to DNA mutations and ultimately influence genome evolution. This review evaluates the ways in which epigenetic information affects genome sequence and evolution. We discuss how DNA methylation has strong and pervasive effects on DNA sequence evolution in eukaryotic organisms. We also review how the physical interactions arising from the connections between histone proteins and DNA affect DNA mutation and repair. We then discuss how a variety of epigenetic mechanisms exert substantial effects on genome evolution by suppressing the movement of transposable elements. Finally, we examine how genome expansion through gene duplication is also partially controlled by epigenetic information. Overall, we conclude that epigenetic information has widespread indirect effects on DNA sequences in eukaryotes and represents a potent cause and constraint of genome evolution.This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

scholarly journals Constrained mutational sampling of amino acids in HIV-1 protease evolution

2018 ◽  
Author(s):  
Jeffrey I. Boucher ◽  
Troy W. Whitfield ◽  
Ann Dauphin ◽  
Gily Nachum ◽  
Carl Hollins ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Protein Sequence ◽  
Fitness Landscape ◽  
Sequence Evolution ◽  
Single Mutation ◽  
The Impact ◽  
Protein Sequence Evolution ◽  
Hiv 1

AbstractThe evolution of HIV-1 protein sequences should be governed by a combination of factors including nucleotide mutational probabilities, the genetic code, and fitness. The impact of these factors on protein sequence evolution are interdependent, making it challenging to infer the individual contribution of each factor from phylogenetic analyses alone. We investigated the protein sequence evolution of HIV-1 by determining an experimental fitness landscape of all individual amino acid changes in protease. We compared our experimental results to the frequency of protease variants in a publicly available dataset of 32,163 sequenced isolates from drug-naïve individuals. The most common amino acids in sequenced isolates supported robust experimental fitness, indicating that the experimental fitness landscape captured key features of selection acting on protease during viral infections of hosts. Amino acid changes requiring multiple mutations from the likely ancestor were slightly less likely to support robust experimental fitness than single mutations, consistent with the genetic code favoring chemically conservative amino acid changes. Amino acids that were common in sequenced isolates were predominantly accessible by single mutations from the likely protease ancestor. Multiple mutations commonly observed in isolates were accessible by mutational walks with highly fit single mutation intermediates. Our results indicate that the prevalence of multiple base mutations in HIV-1 protease is strongly influenced by mutational sampling.

scholarly journals Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 555
Author(s):  
Emily L. Gordon ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
Amino Acids ◽  
Protein Structure ◽  
Amino Acid ◽  
Bird Species ◽  
Data Type ◽  
Substitution Matrix ◽  
Sequence Evolution ◽  
Transmembrane Helices ◽  
Encoded Proteins ◽  
The Impact

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.

scholarly journals Mass Outflow in Molecular Clouds: A New Phase in the Evolution of Newly-Formed Stars?

1983 ◽  
Vol 6 ◽  
pp. 686-706 ◽  
Author(s):  
R. Genzel ◽  
D. Downes
Keyword(s):  
Molecular Clouds ◽  
Sequence Evolution ◽  
Interstellar Clouds ◽  
Physical Conditions ◽  
Long Duration ◽  
Mass Outflow ◽  
Infrared Sources ◽  
T Tau ◽  
The Impact ◽  
New Phase

Molecular gas with velocity dispersions exceeding 100 km s-1 toward dense, interstellar clouds was discovered by microwave observers about a decade ago. It has now been established that this high velocity gas is a result of violent mass outflows (winds) originating from T-Tau stars, compact infrared sources or ultra-compact HII regions at the cores of the clouds. The mass outflow phenomena occur in regions of star formation covering five orders of magnitude in luminosity, and are of long duration . The observations suggest that violent mass loss is a new, important phase in the pre-main sequence evolution of newly-formed stars more massive than a few solar masses. The impact of the flows on the energy balance and dynamical stability of molecular clouds may be substantial. This review is mainly a summary of the observational facts, and gives a description of the physical conditions in an outflow zone. The impact of the flows on molecular clouds is discussed. Recent reviews of the outflow phenomena can also be found in (1, 2, 3, ).

scholarly journals Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy

2020 ◽  
Vol 12 (9) ◽  
pp. 1549-1565
Author(s):  
Kelsey Aadland ◽  
Bryan Kolaczkowski
Keyword(s):  
Sequence Alignment ◽  
Evolutionary Process ◽  
Sequence Evolution ◽  
Sequence Alignments ◽  
Ancestral Sequences ◽  
Structural And Functional Properties ◽  
Sequence Reconstruction ◽  
Alignment Errors ◽  
The Impact ◽  
Alignment Uncertainty

Abstract Ancestral sequence reconstruction (ASR) uses an alignment of extant protein sequences, a phylogeny describing the history of the protein family and a model of the molecular-evolutionary process to infer the sequences of ancient proteins, allowing researchers to directly investigate the impact of sequence evolution on protein structure and function. Like all statistical inferences, ASR can be sensitive to violations of its underlying assumptions. Previous studies have shown that, whereas phylogenetic uncertainty has only a very weak impact on ASR accuracy, uncertainty in the protein sequence alignment can more strongly affect inferred ancestral sequences. Here, we show that errors in sequence alignment can produce errors in ASR across a range of realistic and simplified evolutionary scenarios. Importantly, sequence reconstruction errors can lead to errors in estimates of structural and functional properties of ancestral proteins, potentially undermining the reliability of analyses relying on ASR. We introduce an alignment-integrated ASR approach that combines information from many different sequence alignments. We show that integrating alignment uncertainty improves ASR accuracy and the accuracy of downstream structural and functional inferences, often performing as well as highly accurate structure-guided alignment. Given the growing evidence that sequence alignment errors can impact the reliability of ASR studies, we recommend that future studies incorporate approaches to mitigate the impact of alignment uncertainty. Probabilistic modeling of insertion and deletion events has the potential to radically improve ASR accuracy when the model reflects the true underlying evolutionary history, but further studies are required to thoroughly evaluate the reliability of these approaches under realistic conditions.

scholarly journals Topography Controls N2O Emissions Differently during Early and Late Corn Growing Season

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 187
Author(s):  
Waqar Ashiq ◽  
Hiteshkumar B. Vasava ◽  
Uttam Ghimire ◽  
Prasad Daggupati ◽  
Asim Biswas
Keyword(s):  
Chemical Properties ◽  
Growth Period ◽  
Growing Season ◽  
Crop Growth ◽  
Slope Position ◽  
Agricultural Fields ◽  
N2o Emissions ◽  
Growth Variability ◽  
The Impact ◽  
Upper Slope

Topography affects soil hydrological, pedological, and biochemical processes and may influence nitrous oxide (N2O) emissions into the atmosphere. While N2O emissions from agricultural fields are mainly measured at plot scale and on flat topography, intrafield topographical and crop growth variability alter soil processes and might impact N2O emissions. The objective of this study was to examine the impact of topographical variations on crop growth period dependent soil N2O emissions at the field scale. A field experiment was conducted at two agricultural farms (Baggs farm; BF and Research North; RN) with undulating topography. Dominant slope positions (upper, middle, lower and toeslope) were identified based on elevation difference. Soil and gas samples were collected from four replicated locations within each slope position over the whole corn growing season (May–October 2019) to measure soil physio-chemical properties and N2O emissions. The N2O emissions at BF ranged from −0.27 ± 0.42 to 255 ± 105 g ha−1 d−1. Higher cumulative emissions were observed from the upper slope (1040 ± 487 g ha−1) during early growing season and from the toeslope (371 ± 157 g ha−1) during the late growing season with limited variations during the mid growing season. Similarly, at RN farm, (emissions ranged from −0.50 ± 0.83 to 70 ± 15 g ha−1 d−1), the upper slope had higher cumulative emissions during early (576 ± 132 g ha−1) and mid (271 ± 51 g ha−1) growing season, whereas no impact of slope positions was observed during late growing season. Topography controlled soil and environmental properties differently at different crop growth periods; thus, intrafield variability must be considered in estimating N2O emissions and emission factor calculation from agricultural fields. However, due to large spatial variations in N2O emissions, further explorations into site-specific analysis of individual soil properties and their impact on N2O emissions using multiyear data might help to understand and identify hotspots of N2O emissions.

scholarly journals A 500 kyr record of global sea level oscillations in the Gulf of Lion, Mediterranean Sea: new insights into MIS 3 sea level variability

2011 ◽  
Vol 7 (6) ◽  
pp. 4401-4428
Author(s):  
J. Frigola ◽  
M. Canals ◽  
I. Cacho ◽  
A. Moreno ◽  
F. J. Sierro ◽  
...  
Keyword(s):  
Grain Size ◽  
Sea Level ◽  
High Sensitivity ◽  
Sea Levels ◽  
Gulf Of Lion ◽  
Sea Level Oscillations ◽  
Global Sea Level ◽  
The Impact ◽  
Upper Slope ◽  
Millennial Scale

Abstract. Borehole PRGL1-4 drilled in the upper slope of the Gulf of Lion provides an exceptional record to investigate the impact of Late Pleistocene orbitally-driven glacio-eustatic sea level oscillations on the sedimentary outbuilding of a river fed continental margin. High-resolution grain-size and geochemical records supported by oxygen isotope chronostratigraphy allow reinterpreting the last 500 ka upper slope seismostratigraphy of the Gulf of Lion which consists of five main sequences stacked during the sea level lowering phases of the last five glacial-interglacial 100-kyr cycles. The high sensitivity to sea level oscillations of the grain-size record along the borehole, favoured by the large width of the Gulf of Lion continental shelf, demonstrates that sea level driven changes in accommodation space over the shelf are able to cyclically modify the depositional mode of the entire margin. PRGL1-4 data also illustrate the imprint of sea level oscillations at millennial scale, as shown for Marine Isotopic Stage 3, and provide unambiguous evidence of relative high sea levels at the onset of each Dansgaard-Oeschger Greenland warm interstadial. The PRGL1-4 grain-size record represents the first evidence ever for a one-to-one coupling of millennial-scale sea level oscillations associated with each Dansgaard-Oeschger cycle.

scholarly journals Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

2021 ◽  
Author(s):  
Emily L. Gordon ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
Amino Acids ◽  
Protein Structure ◽  
Transmembrane Protein ◽  
Phylogenetic Analyses ◽  
Bird Species ◽  
Data Type ◽  
Sequence Evolution ◽  
Transmembrane Helices ◽  
Encoded Proteins ◽  
The Impact

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acids exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution dataset for transmembrane helices from a variety of sampled set of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.

Sign in / Sign up

Export Citation Format

Share Document