scholarly journals Predicting the genetic loci of past evolution

2017 ◽  
Author(s):  
Virginie Courtier-Orgogozo ◽  
Arnaud Martin
Keyword(s):  
Genetic Evolution ◽  
Genetic Loci ◽  
Nucleotide Level ◽  
Genetic Changes ◽  
The Past ◽  
Independent Evolution ◽  
Evolutionary Changes ◽  
Gene Level ◽  
Regulatory Mutations

AbstractRepetitions in the mutations found to be responsible for independent evolution of similar phenotypes in various taxa have led some biologists to propose that for certain evolutionary changes the causal mutations are predictable. We examine here the nature of the predictions that have been made and their associated arguments. Predictions about the loci of past evolution are retrodictions, i.e. inferences about events that occurred in the past. They are not based on elaborate models and they derive mainly from the observation of repeated cases of genetic evolution. Predictions at the nucleotide level or at the gene level have a higher inference gain than those for broader categories of genetic changes such as cis-regulatory mutations.

scholarly journals Identifying drivers of parallel evolution: A regression model approach

2017 ◽  
Author(s):  
Susan F. Bailey ◽  
Qianyun Guo ◽  
Thomas Bataillon
Keyword(s):  
Evolutionary Biology ◽  
Empirical Studies ◽  
Parallel Evolution ◽  
Published Data ◽  
Genetic Changes ◽  
Selective Pressures ◽  
Evolutionary Changes ◽  
Gene Level ◽  
Peer Community ◽  
Mutation And Selection

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100045). Parallel evolution, defined as identical changes arising in independent populations, is often attributed to similar selective pressures favoring the fixation of identical genetic changes. However, some level of parallel evolution is also expected if mutation rates are heterogeneous across regions of the genome. Theory suggests that mutation and selection can have equal impacts on patterns of parallel evolution, however empirical studies have yet to jointly quantify the importance of these two processes. Here, we introduce several statistical models to examine the contributions of mutation and selection heterogeneity to shaping parallel evolutionary changes at the gene-level. Using this framework we analyze published data from forty experimentally evolved Saccharomyces cerevisiae populations. We can partition the effects of a number of genomic variables into those affecting patterns of parallel evolution via effects on the rate of arising mutations, and those affecting the retention versus loss of the arising mutations (i.e. selection). Our results suggest that gene-to-gene heterogeneity in both mutation and selection, associated with gene length, recombination rate, and number of protein domains drive parallel evolution at both synonymous and nonsynonymous sites. While there are still a number of parallel changes that are not well described, we show that allowing for heterogeneous rates of mutation and selection can provide improved predictions of the prevalence and degree of parallel evolution.Data archival locationDryad, doi to be included later

scholarly journals Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution

2012 ◽  
Vol 93 (9) ◽  
pp. 1996-2007 ◽  
Author(s):  
Kim B. Westgeest ◽  
Miranda de Graaf ◽  
Mathieu Fourment ◽  
Theo M. Bestebroer ◽  
Ruud van Beek ◽  
...  
Keyword(s):  
Humoral Immunity ◽  
Influenza A ◽  
Phylogenetic Trees ◽  
Influenza Viruses ◽  
Genetic Maps ◽  
Genetic Evolution ◽  
Human Influenza ◽  
Nucleotide Level ◽  
Antigenic Evolution ◽  
Positively Selected Sites

Each year, influenza viruses cause epidemics by evading pre-existing humoral immunity through mutations in the major glycoproteins: the haemagglutinin (HA) and the neuraminidase (NA). In 2004, the antigenic evolution of HA of human influenza A (H3N2) viruses was mapped (Smith et al., Science 305, 371–376, 2004) from its introduction in humans in 1968 until 2003. The current study focused on the genetic evolution of NA and compared it with HA using the dataset of Smith and colleagues, updated to the epidemic of the 2009/2010 season. Phylogenetic trees and genetic maps were constructed to visualize the genetic evolution of NA and HA. The results revealed multiple reassortment events over the years. Overall rates of evolutionary change were lower for NA than for HA1 at the nucleotide level. Selection pressures were estimated, revealing an abundance of negatively selected sites and sparse positively selected sites. The differences found between the evolution of NA and HA1 warrant further analysis of the evolution of NA at the phenotypic level, as has been done previously for HA.

scholarly journals Inferring recent evolutionary changes in speech sounds

2021 ◽  
Vol 376 (1824) ◽  
Author(s):  
Steven Moran ◽  
Nicholas A. Lester ◽  
Eitan Grossman
Keyword(s):  
Language Contact ◽  
Language Evolution ◽  
Speech Sounds ◽  
Theme Issue ◽  
Short Term ◽  
The Past ◽  
Evolutionary Changes ◽  
The One ◽  
The Impact

In this paper, we investigate evolutionarily recent changes in the distributions of speech sounds in the world's languages. In particular, we explore the impact of language contact in the past two millennia on today's distributions. Based on three extensive databases of phonological inventories, we analyse the discrepancies between the distribution of speech sounds of ancient and reconstructed languages, on the one hand, and those in present-day languages, on the other. Furthermore, we analyse the degree to which the diffusion of speech sounds via language contact played a role in these discrepancies. We find evidence for substantive differences between ancient and present-day distributions, as well as for the important role of language contact in shaping these distributions over time. Moreover, our findings suggest that the distributions of speech sounds across geographic macro-areas were homogenized to an observable extent in recent millennia. Our findings suggest that what we call the Implicit Uniformitarian Hypothesis, at least with respect to the composition of phonological inventories, cannot be held uncritically. Linguists who would like to draw inferences about human language based on present-day cross-linguistic distributions must consider their theories in light of even short-term language evolution. This article is part of the theme issue ‘Reconstructing prehistoric languages’.

scholarly journals Molecular function limits divergent protein evolution on planetary timescales

2017 ◽  
Author(s):  
Mariam M. Konaté ◽  
Germán Plata ◽  
Jimin Park ◽  
Dinara R. Usmanova ◽  
Harris H. Wang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Evolution ◽  
Molecular Function ◽  
Functional Conservation ◽  
Fitness Effects ◽  
Sequence Identity ◽  
The Past ◽  
Independent Evolution

AbstractFunctional conservation is known to constrain protein evolution. Nevertheless, the long-term divergence patterns of proteins maintaining the same molecular function and the possible limits of this divergence have not been explored in detail. We investigate these fundamental questions by characterizing the divergence between ancient protein orthologs with conserved molecular function. Our results demonstrate that the decline of sequence and structural similarities between such orthologs significantly slows down after ~1-2 billion years of independent evolution. As a result, their sequence and structural similarities have not substantially decreased for the past billion years. The effective divergence limit (>25% sequence identity) is not primarily due to protein sites universally conserved in all linages. Instead, less than four amino acid types are accepted, on average, per site in orthologs strictly conserving their molecular function. Our analysis also reveals different divergence patterns for protein sites with experimentally determined small and large fitness effects of mutations.

scholarly journals Evolutionary Changes of the flhDC Flagellar Master Operon in Shigella Strains

2005 ◽  
Vol 187 (12) ◽  
pp. 4295-4302 ◽  
Author(s):  
Akira Tominaga ◽  
Ruiting Lan ◽  
Peter R. Reeves
Keyword(s):  
Dna Sequences ◽  
Gene Clusters ◽  
Housekeeping Gene ◽  
Genetic Damage ◽  
Flagellar Motility ◽  
Genetic Changes ◽  
Mutational Change ◽  
E Coli ◽  
Evolutionary Changes ◽  
Cluster 2

ABSTRACT Shigella strains are nonmotile. The master operon of flagellar synthesis, flhDC, was analyzed for genetic damage in 46 Shigella strains representing all known serotypes. In 11 strains (B1, B3, B6, B8, B10, B18, D5, F1B, D10, F3A, and F3C) the flhDC operon was completely deleted. PCR and sequence analysis of the flhDC region of the remaining 35 strains revealed many insertions or deletions associated with insertion sequences, and the majority of the strains were found to be defective in their flhDC genes. As these genes also play a role in regulation of nonflagellar genes, the loss may have other consequences or be driven by selection pressures other than those against flagellar motility. It has been suggested that Shigella strains fall mostly into three clusters within Escherichia coli, with five outlier strains, four of which are also within E. coli (G. M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567-10572, 2000). The distribution of genetic changes in the flhDC region correlated very well with the three clusters and outlier strains found using housekeeping gene DNA sequences, enabling us to follow the sequence of mutational change in the flhDC locus. Two cluster 2 strains were found to have unique flhDC sequences, which are most probably due to recombination during the exchange of the adjacent O-antigen gene clusters.

scholarly journals Reflections on practice: A virally-infected curriculum must adapt or suffer!

2021 ◽  
Vol 22 (1) ◽  
pp. 88-93
Author(s):  
Christian Cobbold ◽  
Louise Wright
Keyword(s):  
Medical Education ◽  
Active Learning ◽  
Viral Infection ◽  
Student Feedback ◽  
Genetic Evolution ◽  
Evolutionary Changes ◽  
Medical Program ◽  
Education Delivery

Viruses are recognised for their ability to induce genetic evolution and cause disease. SARS-CoV-2 has catalysed rapid evolutionary changes in the delivery of preclinical teaching of the Griffith University medical program across diverse sites by inducing the use of progressive student feedback to enhance active learning in an online flipped format. These COVID-induced adaptations in medical education delivery, innovation and fast-tracked modernisation are, unlike viral infection, a curve that we embrace and do not want to squash.

scholarly journals Evolution of Human Longevity and the Genetic Complexity Governing Aging Rate

2001 ◽  
Vol 2001 (1) ◽  
Author(s):  
Richard G. Cutler
Keyword(s):  
Life Span ◽  
Maximum Rate ◽  
Human Longevity ◽  
Maximum Life Span ◽  
Genetic Changes ◽  
Aging Rate ◽  
The Past ◽  
Time Period ◽  
Rate Of Increase ◽  
Genetic Complexity

The genetic complexity of processes governing the aging rate of humans was estimated by determining the maximum rate at which life-span has evolved along the hominid ancestral-descendant sequence. Maximum life-span potential was found to have increased approximately twofold over the past 3 million years, reaching a maximum rate of increase of 14 years per 100,000 years about 100,000 years ago. It is estimated that about 0.6% of the total functional genes have received substitutions leading to one or more adaptive amino acid changes during this 100,000-year time-period. This suggests that aging is not the result of the expression of a large number of independently acting processes. Instead, primary aging processes appear to exist in which only a few genetic changes are necessary to uniformly decrease the aging rate of many different physiological functions. Reproduced by permission. Richard G. Cutler, Evolution of Human Longevity and the Genetic Complexity Governing Aging Rate. Proc. Natl. Acad. Sci. U.S.A. 72 , 4664-4668 (1975).

scholarly journals The Genetic Changes of Hepatoblastoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Huitong Chen ◽  
Qian Guan ◽  
Huiqin Guo ◽  
Lei Miao ◽  
Zhenjian Zhuo
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genetic Syndromes ◽  
Disease Treatment ◽  
Single Nucleotide ◽  
Genetic Changes ◽  
Future Studies ◽  
The Past ◽  
Malignant Liver ◽  
Genetic Events ◽  
Made In

Hepatoblastoma is the most common malignant liver cancer in childhood. The etiology of hepatoblastoma remains obscure. Hepatoblastoma is closely related to genetic syndromes, hinting that hepatoblastoma is a genetic predisposition disease. However, no precise exposures or genetic events are reported to hepatoblastoma occurrence. During the past decade, significant advances have been made in the understanding of etiology leading to hepatoblastoma, and several important genetic events that appear to be important for the development and progression of this tumor have been identified. Advances in our understanding of the genetic changes that underlie hepatoblastoma may translate into better patient outcomes. Single nucleotide polymorphisms (SNPs) have been generally applied in the research of etiology’s exploration, disease treatment, and prognosis assessment. Here, we reviewed and discussed the molecular epidemiology, especially SNPs progresses in hepatoblastoma, to provide references for future studies and promote the study of hepatoblastoma’s etiology.

scholarly journals Prediction and Recommendation of Precision Medicine for Cancer using Machine Learning Techniques

2019 ◽  
Vol 9 (2) ◽  
pp. 792-795
Keyword(s):  
Machine Learning ◽  
Precision Medicine ◽  
Genetic Model ◽  
Machine Learning Techniques ◽  
Genetic Profile ◽  
Gene Expressions ◽  
Genetic Changes ◽  
The Past ◽  
Learning Techniques ◽  
Near Future

Cancer is one of the major causes of death by disease and treatment of cancer is one of the most crucial phases of oncology. Precision medicine for cancer treatment is an approach that uses the genetic profile of individual patients. Researchers have not yet discovered all the genetic changes that causes cancer to develop, grow and spread. The Neuro-Genetic model is proposed here for the prediction and recommendation of precision medicine. The proposed work attempts to recommend precision medicine to cancer patients based upon the past genomic data of patient’s survival. The work will employ machine learning (ML) approaches to provide recommendations for different gene expressions. This work can be used in caner hospitals, research institutions for providing personalized treatment to the patient using precision medicine. Precision medicine can even be used to treat other complex diseases like diabetes, dentistry, cardiovascular diseases etc. Precision medicine is the kind of treatment to be offered in the near future.

Evolution at All Scales in the Vertebrate Fossil Record

2002 ◽  
Vol 11 ◽  
pp. 165-178
Author(s):  
John P. Hunter
Keyword(s):  
Fossil Record ◽  
Large Scale ◽  
Large Time ◽  
Evolutionary Change ◽  
Theory Of Evolution ◽  
Evolutionary Forces ◽  
The Past ◽  
Evolutionary Changes ◽  
Abundant Evidence ◽  
Transitional Forms

The fossil record of vertebrates provides abundant evidence for both the fact and the theory of evolution (Carroll, 1997; Prothero and Schoch, 1994). In support of the fact that evolution has indeed occurred, the vertebrate fossil record clearly documents evolutionary change along lineages, that is, along direct lines of ancestors and descendents. The fossil record also shows step-wise evolutionary changes resulting in the emergence of new kinds of vertebrates from pre-existing kinds—for example, the origin of mammals from the “mammal-like” reptiles. In support of the theory that natural selection, in particular, has been largely responsible for evolutionary change, the fossil record shows that the numerous “transitional” forms that lived in the past—far from being nonviable “monsters”—were functionally integrated organisms that were well adapted to their ecological roles. Finally, the vertebrate fossil record preserves certain large-scale phenomena, such as radiations and trends, which show that evolutionary forces can act over very large time scales.

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