scholarly journals Protein Evolution Depends on Multiple Distinct Population Size Parameters

2017 ◽  
Author(s):  
Alexander Platt ◽  
Claudia C Weber ◽  
David A Liberles
Keyword(s):  
Population Size ◽  
Protein Evolution ◽  
Functional Constraints ◽  
Effective Population ◽  
Coding Sequences ◽  
The Many ◽  
Definition Of ◽  
Evolution Of Proteins ◽  
The Relationship ◽  
New Mutations

AbstractThat population size affects the fate of new mutations arising in genomes, modulating both how frequently they arise and how efficiently natural selection is able to filter them, is well established. It is therefore clear that these distinct roles for population size that characterize different processes should affect the evolution of proteins and need to be carefully defined. Empirical evidence is consistent with a role for demography in influencing protein evolution, supporting the idea that functional constraints alone do not determine the composition of coding sequences.Given that the relationship between population size, mutant fitness and fixation probability has been well characterized, estimating fitness from observed substitutions is well within reach with well-formulated models. Molecular evolution research has, therefore, increasingly begun to leverage concepts from population genetics to quantify the selective effects associated with different classes of mutation. However, in order for this type of analysis to provide meaningful information about the intra- and inter-specific evolution of coding sequences, a clear definition of concepts of population size, what they influence, and how they are best parameterized is essential.Here, we present an overview of the many distinct concepts that “population size” and “effective population size” may refer to, what they represent for studying proteins, and how this knowledge can be harnessed to produce better specified models of protein evolution.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes

2020 ◽  
Vol 12 (12) ◽  
pp. 2441-2449
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Range Size ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

Abstract What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.

Examination of the relationship between inbreeding and population size

1985 ◽  
Vol 17 (1) ◽  
pp. 97-106 ◽  
Author(s):  
John H. Relethford
Keyword(s):  
Population Structure ◽  
Linear Regression ◽  
Population Size ◽  
Effective Population Size ◽  
Linear Regression Model ◽  
Historical Change ◽  
Human Populations ◽  
Effective Population ◽  
The Common ◽  
The Relationship

SummaryA method is presented for examining the relationship between effective population size and accumulated random inbreeding in human populations. For a set of populations, the inverse of inbreeding is regressed on effective population size using a linear regression model. This procedure allows testing of several hypotheses regarding the common and unique influences on population structure. Deviations from the expected curve suggest demographic or historical change. This method is applied to surname data from nine Irish isolates. The results show that the method is very useful in assessing differential influences on population structure.

Domestic violence in pregnancy

2001 ◽  
Vol 12 (4) ◽  
pp. 249-271 ◽  
Author(s):  
Loraine Bacchus ◽  
Susan Bewley ◽  
Gill Mezey
Keyword(s):  
Domestic Violence ◽  
Emotional Abuse ◽  
Physical Violence ◽  
Female Partners ◽  
Living Together ◽  
The Many ◽  
Definition Of ◽  
Demographic Patterns ◽  
And Control ◽  
The Relationship

Definitions of domestic violence vary according to the frequency, severity and nature of the violence as well as the context in which it occurred and the relationship between the victim and the perpetrator. Though there is a lack of uniformity, a generally accepted definition of domestic violence is the physical, sexual or emotional abuse of an adult woman by a man with whom she has or has had an intimate relationship, regardless of whether the couple are living together. Although violence can be carried out by other family members or occur in same-sex relationships, it is argued that men use violence in order to maintain dominance and control over their female partners. Physical violence is just one of the many tactics that an abuser may use to exert control over his partner. Other behaviours include isolation, intimidation, threats of violence, threats to take the children away or hurt them and emotional or economic abuse. Whilst some studies have identified demographic patterns associated with domestic violence, it can affect any woman regardless of age, race, ethnicity, social class, employment status, religion, marital status or disability.

scholarly journals Spread of new mutations through space

2022 ◽  
Author(s):  
Kyle Shaw ◽  
Peter Beerli
Keyword(s):  
Population Density ◽  
Population Size ◽  
Simulation Software ◽  
Effective Population ◽  
Random Drift ◽  
Rate Of Spread ◽  
Large Populations ◽  
Discrete Population ◽  
Explicit Simulation ◽  
New Mutations

The terms population size and population density are often used interchangeably, when in fact they are quite different. When viewed in a spatial landscape, density is defined as the number of individuals within a square unit of distance, while population size is simply the total count of a population. In discrete population genetics models, the effective population size is known to influence the interaction between selection and random drift with selection playing a larger role in large populations while random drift has more influence in smaller populations. Using a spatially explicit simulation software we investigate how population density affects the flow of new mutations through a geographical space. Using population density, selectional advantage, and dispersal distributions, a model is developed to predict the speed at which the new allele will travel, obtaining more accurate results than current diffusion approximations provide. We note that the rate at which a neutral mutation spreads begins to decay over time while the rate of spread of an advantageous allele remains constant. We also show that new advantageous mutations spread faster in dense populations.

The Genetic Effective Size of a Population

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Structure ◽  
Population Subdivision ◽  
Effective Population ◽  
Entire Genome ◽  
History Of ◽  
A Site ◽  
The Hill ◽  
New Mutations

The effects of genetic drift usually assume an idealized population of constant size. This chapter shows how the population size for such an idealized population can be replaced with an effective population size for populations with age structure, unequal sex ratios, a history of expansion or contraction, inbreeding, and population subdivision. These demographic features impact the entire genome more or less equally. A relatively recent understanding is that selection at a site can dramatically reduce the local effective population size experienced by nearby linked sites (the Hill-Robertson effect). This can arise from background selection to remove deleterious new mutations or from selective sweeps wherein favorable new mutations are driven toward fixation. The Hill-Robertson effect is a general way to describe the fact that selection at a site makes selection are other linked sites less efficient, and, therefore, more neutral. This chapter discusses the implications of this finding for genome structure.

scholarly journals Evidences of delayed size recovery in Araucaria angustifolia populations after post-glacial colonization of highlands in Southeastern Brazil

2008 ◽  
Vol 80 (3) ◽  
pp. 433-443 ◽  
Author(s):  
Valdir M. Stefenon ◽  
Hermann Behling ◽  
Oliver Gailing ◽  
Reiner Finkeldey
Keyword(s):  
Population Size ◽  
Demographic History ◽  
Southeastern Brazil ◽  
Effective Population ◽  
History Of ◽  
Natural Stands ◽  
Recovery Dynamics ◽  
The Relationship ◽  
Palynological Records ◽  
Small Effective Population Size

Up to date, little is known about the relationship between historical demography and the current genetic structure of A. Angus As a first effort towards overcoming this lack, microsatellite data scored in six populations and isozyme allele frequencies published for 11 natural stands of this species were analysed in order to assess molecular signatures of populations' demographic history. Signatures of genetic bottlenecks were captured in all analysed populations of southeastern Brazil. Among southern populations, signatures of small effective population size were observed in only three out of 13 populations. Southern populations likely experienced faster recovery of population size after migration onto highlands. Accordingly, current genetic diversity of the southern populations gives evidence of fast population size recovery. In general, demographic history of A. Angusmatches climatic dynamics of southern and southeastern Brazil during the Pleistocene and Holocene. Palynological records and reconstruction of the past climatic dynamics of southeastern and southern Brazil support the hypothesis of different population size recovery dynamics for populations from these regions.

Legal Uses of Anthropology in France in the Nineteenth and Twentieth Centuries

2021 ◽  
Author(s):  
Frédéric Audren ◽  
Laetitia Guerlain
Keyword(s):  
Social Sciences ◽  
Legal Positivism ◽  
Legal Anthropology ◽  
The Past ◽  
Human And Social Sciences ◽  
History Of ◽  
Nineteenth And Twentieth Centuries ◽  
The Many ◽  
Definition Of ◽  
The Relationship

This chapter sheds light on the long-standing history of the relationship between law and the human and social sciences in nineteenth- and twentieth-century France. This story has often been reduced to its most recent and academic development, that is, legal anthropology. However, focusing on this strictly contemporary, academic definition of anthropology risks overlooking the many and varied ways of thinking that, over the past two centuries and more, have shaped the relationship between law and the study of humanity. The authors suggest that such an approach obscures the depth and the variety of forms that this relationship took over time. This chapter documents the various ways that legal scholars in France—over the course of two centuries marked by the rise of codification and legal positivism—drew upon history, philology, ethnology, physical anthropology, and sociology, all in the pursuit of a more profound understanding of homo juridicus.

scholarly journals The Entropy Universe

Entropy ◽  
2021 ◽  
Vol 23 (2) ◽  
pp. 222 ◽  
Author(s):  
Maria Ribeiro ◽  
Teresa Henriques ◽  
Luísa Castro ◽  
André Souto ◽  
Luís Antunes ◽  
...  
Keyword(s):  
Time Series ◽  
Mathematical Linguistics ◽  
Research Field ◽  
Research Areas ◽  
The Many ◽  
Definition Of ◽  
Novel Applications ◽  
Number Of Citations ◽  
The Relationship ◽  
Scientific Fields

About 160 years ago, the concept of entropy was introduced in thermodynamics by Rudolf Clausius. Since then, it has been continually extended, interpreted, and applied by researchers in many scientific fields, such as general physics, information theory, chaos theory, data mining, and mathematical linguistics. This paper presents The Entropy Universe, which aims to review the many variants of entropies applied to time-series. The purpose is to answer research questions such as: How did each entropy emerge? What is the mathematical definition of each variant of entropy? How are entropies related to each other? What are the most applied scientific fields for each entropy? We describe in-depth the relationship between the most applied entropies in time-series for different scientific fields, establishing bases for researchers to properly choose the variant of entropy most suitable for their data. The number of citations over the past sixteen years of each paper proposing a new entropy was also accessed. The Shannon/differential, the Tsallis, the sample, the permutation, and the approximate entropies were the most cited ones. Based on the ten research areas with the most significant number of records obtained in the Web of Science and Scopus, the areas in which the entropies are more applied are computer science, physics, mathematics, and engineering. The universe of entropies is growing each day, either due to the introducing new variants either due to novel applications. Knowing each entropy’s strengths and of limitations is essential to ensure the proper improvement of this research field.

scholarly journals Beyond Translation Proper—Extending the Field of Translation Studies

2008 ◽  
Vol 20 (1) ◽  
pp. 281-308 ◽  
Author(s):  
Karen Korning Zethsen
Keyword(s):  
Empirical Research ◽  
Modern Society ◽  
Translation Studies ◽  
Translation Theory ◽  
Modern Life ◽  
Ulterior Motive ◽  
Similarities And Differences ◽  
The Many ◽  
Definition Of ◽  
The Relationship

Abstract Modern society demands many different kinds of translation or translation-like activities which often exceed the boundaries of what translation theory traditionally terms translation proper. Highly functional translations, localisation, précis-writing, expert-to-layman communication, etc. are all part of modern life, but where do such activities fit in theoretically? In this article I shall discuss the fact that despite Jakobson’s classical definition, intralingual translation or rewording is de facto peripheral to translation studies and I shall argue that the relationship between interlingual and intralingual translation is a neglected area of research, as is a thorough description of intralingual translation. Since Jakobson’s definition, general definitions of translation have become less inclusive. This I consider a major setback as there seems to be much to gain theoretically as well as practically by looking for similarities and differences between various kinds of translational activities. With the ulterior motive of putting intralingual translation (back?) on the map of translation studies and to encourage future empirical research within this area I shall argue for a broader perception of translation and consequently of translation studies as a discipline. Inspired by Jakobson (1959), Toury (1995) and Tymoczko (1998, 2005), I shall attempt to draw up an open definition of translation which reflects the many-faceted nature of the phenomenon.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: a Correlation Between the Effective and Census Population Sizes

2020 ◽  
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Diversity ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

AbstractWhat determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Since, neutral diversity depends upon the product of the effective population size and mutation rate there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest dataset to date from 639 mammalian species. In a multiple regression we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of non-synonymous to synonymous diversity, is also significantly negatively correlated to both range and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12 to 20%, providing one of the first quantifications of the relationship between effective and census population sizes.

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