scholarly journals Studying mutation rate evolution in primates—the effects of computational pipelines and parameter choices

GigaScience ◽  
2021 ◽  
Vol 10 (10) ◽  
Author(s):  
Susanne P Pfeifer
Keyword(s):  
Rhesus Macaque ◽  
Mutation Rate ◽  
Recent Article ◽  
Computational Pipeline ◽  
Rate Estimation ◽  
Mutation Rate Estimation ◽  
Mutational Process ◽  
Mutation Rate Evolution

Abstract This commentary investigates the important role of computational pipeline and parameter choices in performing mutation rate estimation, using the recent article published in this journal by Bergeron et al. entitled “The germline mutational process in rhesus macaque and its implications for phylogenetic dating” as an illustrative example.

scholarly journals Upper-limit mutation rate estimation for a plant RNA virus

2009 ◽  
Vol 5 (3) ◽  
pp. 394-396 ◽  
Author(s):  
Rafael Sanjuán ◽  
Patricia Agudelo-Romero ◽  
Santiago F. Elena
Keyword(s):  
Mutation Rate ◽  
Rna Viruses ◽  
Rna Virus ◽  
Plant Viruses ◽  
Mutation Rates ◽  
Methodological Error ◽  
Direct Estimate ◽  
Rate Estimation ◽  
Mutation Rate Estimation

It is generally accepted that mutation rates of RNA viruses are inherently high due to the lack of proofreading mechanisms. However, direct estimates of mutation rate are surprisingly scarce, in particular for plant viruses. Here, based on the analysis of in vivo mutation frequencies in tobacco etch virus , we calculate an upper-bound mutation rate estimation of 3×10 −5 per site and per round of replication; a value which turns out to be undistinguishable from the methodological error. Nonetheless, the value is barely on the lower side of the range accepted for RNA viruses, although in good agreement with the only direct estimate obtained for other plant viruses. These observations suggest that, perhaps, differences in the selective pressures operating during plant virus evolution may have driven their mutation rates towards values lower than those characteristic of other RNA viruses infecting bacteria or animals.

scholarly journals The germline mutational process in rhesus macaque and its implications for phylogenetic dating

2020 ◽  
Author(s):  
Lucie A. Bergeron ◽  
Søren Besenbacher ◽  
Jaco Bakker ◽  
Jiao Zheng ◽  
Panyi Li ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Mutation Rate ◽  
De Novo ◽  
Rhesus Macaques ◽  
Average Rate ◽  
Paternal Age ◽  
Divergence Times ◽  
Sequencing Coverage ◽  
Parental Bias ◽  
Mutational Process

AbstractUnderstanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ca. 76X per individual, and estimated an average rate of 0.77 × 10−8de novo mutations per site per generation (95 % CI: 0.69 × 10−8 - 0.85 × 10−8). By phasing 50 % of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed an average of 81 % of the de novo mutations, with a trend of an increasing male contribution for older fathers. About 3.5 % of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated based on the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecidae/Hominoidea molecular divergence dated at 52 Mya using our new estimate of the yearly mutation rate.

scholarly journals Complexities of Viral Mutation Rates

2018 ◽  
Vol 92 (14) ◽  
Author(s):  
Kayla M. Peck ◽  
Adam S. Lauring
Keyword(s):  
Population Genetics ◽  
Mutation Rate ◽  
Mutation Rates ◽  
Rate Estimation ◽  
Viral Mutation ◽  
Context Dependent ◽  
Mutation Rate Estimation

ABSTRACT Many viruses evolve rapidly. This is due, in part, to their high mutation rates. Mutation rate estimates for over 25 viruses are currently available. Here, we review the population genetics of virus mutation rates. We specifically cover the topics of mutation rate estimation, the forces that drive the evolution of mutation rates, and how the optimal mutation rate can be context-dependent.

scholarly journals Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China

Meta Gene ◽  
2015 ◽  
Vol 5 ◽  
pp. 150-156 ◽  
Author(s):  
Zhuo Zhao ◽  
Jie Zhang ◽  
Hua Wang ◽  
Zhi-Peng Liu ◽  
Ming Liu ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Large Population ◽  
Mainland China ◽  
Rate Estimation ◽  
Str Loci ◽  
Autosomal Str ◽  
Mutation Rate Estimation

The Eighteenth-Century Social Order in Surat: A Reply and an Excursus on the Riots of 1788 and 1795

1991 ◽  
Vol 25 (2) ◽  
pp. 321-365 ◽  
Author(s):  
Lakshmi Subramanian
Keyword(s):  
Eighteenth Century ◽  
Social Structure ◽  
Social Order ◽  
Recent Article ◽  
Alternative Explanation ◽  
Archival Material ◽  
The Social

The Banias of eighteenth-century Surat, whom Michelguglielmo Torri earlier treated with indifference if not innocence, have invited his wrath since they were brought into focus by the publication of my essay on the Banias and the Surat riot of 1795. In his ‘rejoinder’ to my article, he seeks to wish away their existence altogether (to him there was no specific Bania community, the term merely signifying traders of all communities engaged in the profession of brokerage), and seeks to provide what he regards as an ‘alternative’ explanation of the Muslim–Bania riot of 1795. the Muslim-Bania riot of 1795. It shall be my purpose in this reply to show that his alternative explanation is neither an alternative nor even an explanation, and is based on a basic confusion in his mind about the Banias as well as the principal sources of tension in the social structure of Surat. I shall treat two main subjects in this reply to his misdirected criticisms. First, I shall present some original indigenous material as well as European documentation to further clarify the identity, position and role of the Banias, whom Irfan Habib in a recent article has identified as the most important trading group in the trading world of seventeenth and eighteenth-century India. It is also my purpose to show how the social order of Surat operated under stress by presenting some archival material, the existence of which Torri seems to be completely unaware of, on the Parsi-Muslim riot of 1788.

scholarly journals The role of mutation rate in a simple colonization model

2004 ◽  
Vol 337 (3-4) ◽  
pp. 555-564 ◽  
Author(s):  
R. Huerta-Quintanilla ◽  
M. Rodrı́guez-Achach
Keyword(s):  
Mutation Rate ◽  
Colonization Model

scholarly journals A Computational Pipeline to Design BH3-Mimetic Peptide Inhibitors that Can Bind Specifically to Mcl-1 Or Bcl-XL: Role of Non-Hotspot Residues

2021 ◽  
Vol 120 (3) ◽  
pp. 177a-178a
Author(s):  
Narendra Reddy C ◽  
Nishat Manzar ◽  
Bushra Ateeq ◽  
Ramasubbu Sankararamakrishnan
Keyword(s):  
Peptide Inhibitors ◽  
Computational Pipeline ◽  
Mimetic Peptide ◽  
Bh3 Mimetic

scholarly journals Feasibility Study of Designing and Implementing Performance Budgeting in the Iranian Public Universities and Academic Institutions: The Case of the Sharif University of Thechnology

2013 ◽  
Vol 5 (3) ◽  
pp. 229-235
Author(s):  
Bita Mashayekhi ◽  
Seyed Mostafa SeyedHosseini ◽  
Navid Attaran
Keyword(s):  
Feasibility Study ◽  
Recent Article ◽  
Public Universities ◽  
Academic Institutions ◽  
Performance Budgeting

The role of budgeting in governmental universities is vital since it affects youth generation. According to recent article  passed by education ministry of Iran fundamental changes in universities management is required. In this study Sharif University of Thechnology has been chosen as a case study, obstacles in are identified and relatively a solution is proposed. The result indicates the necessity of implementing performance budgeting in this university.

Being an Archdeacon: A Coaching Model

2020 ◽  
Vol 22 (3) ◽  
pp. 314-327
Author(s):  
Norman Boakes
Keyword(s):  
Recent Article ◽  
Church Of England ◽  
Legal Aspect ◽  
Well Being ◽  
Coaching Model ◽  
Training Development ◽  
Anglican Theology ◽  
The Church ◽  
The Way

Considering the importance of their role in the life of the Church of England and the Church in Wales, there is not much written about the role of archdeacons. In her recent article in the January 2019 issue of this Journal, Jane Steen focused on the legal aspect of the role of archdeacons, and reflected on how they play a key role in shaping the Church and its ministry, delighting in its beauty and rejoicing in its well-being. In this article, the recently retired training, development and support officer for archdeacons reflects on the nature of the role and, in the light of that, on the way in which it might best be carried out. Believing that process is at least as important as outcome, and that good processes lead to better outcomes, he argues that coaching provides a useful model to enable archdeacons to exercise their ministries most effectively and promote both the mission and the well-being of the Church. It is also, he argues, a better reflection of Anglican theology.

Sign in / Sign up

Export Citation Format

Share Document