scholarly journals Microbiomes, Community Ecology, and the Comparative Method

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Sarah M. Hird
Keyword(s):  
Statistical Models ◽  
Comparative Method ◽  
Evolutionary Process ◽  
Biological Information ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Models ◽  
Microbial Biodiversity ◽  
Holistic Understanding ◽  
Ecological Theories ◽  
Host Evolution

ABSTRACT Microbiomes contain many levels of biological information, and integrating across the levels creates a holistic understanding of host-microbiome interactions. In my research on the evolution and ecology of avian microbiomes, I use two complementary frameworks: the microbiome as a community and the microbiome as a trait of the host. We draw on classic ecological and evolutionary theory and modern statistical models to advance our understanding in each of these frameworks and then integrate what we have learned into a better understanding of host-associated microbiomes, host evolution, and microbial biodiversity. Ecological theories that bear on processes such as community assembly and metacommunities are well suited for application to microbiomes. Phylogenetic comparative methods can quantify the fit of evolutionary models and detect correlations between traits and correlations between traits and the rate of evolution; these methods allow the inference of evolutionary process from contemporary patterns.

The place of the plant world in the worldview system of transoxiana sufism in 16th century

2020 ◽  
Vol 6 (Extra-A) ◽  
pp. 157-161
Author(s):  
Lutfullo Eshonovich Ismoilov ◽  
Ramil Tagirovich Yuzmukhametov ◽  
Markhabo Tukhtasunovna Rajabova
Keyword(s):  
Comparative Method ◽  
Literary Analysis ◽  
Semantic Interpretation ◽  
16Th Century ◽  
Main Method ◽  
Holistic Understanding ◽  
The World ◽  
Lives Of The Saints

The article considers the topic of the Plant World in the Sufi writings of the 16th century Transoxiana, based on the material of manakibs, i. e. the so-called Lives of the Saints. The significance and relevance of the topic is due to the need to study the issues of semantic interpretation of the concept of plant and plant world in Sufi writings. Hence, the purpose of this article is to disclose the diverse meanings of the concept of the “World of Plants” contained in the 16th-century Transoxiana manakibs of such authors as Abdurakhman Jami, Abu-l Baka b. Khodzha Bakha-ud-din, Khusein Serakhsi. The main method in the study of this issue is the historical and comparative method, and the method of literary analysis, which allows you to create a holistic understanding of the symbolism of the Plant World in Sufi writings of Transoxiana of the 16th century.      

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

It is not evolutionary models, but models in general that social science needs

2006 ◽  
Vol 29 (4) ◽  
pp. 351-352 ◽  
Author(s):  
Bruce Bridgeman
Keyword(s):  
Social Sciences ◽  
Social Science ◽  
Mathematical Models ◽  
Cultural Models ◽  
Genetic Models ◽  
Biological Information ◽  
Evolutionary Models ◽  
Cultural Information

Mathematical models are potentially as useful for culture as for evolution, but cultural models must have different designs from genetic models. Social sciences must borrow from biology the idea of modeling, rather than the structure of models, because copying the product is fundamentally different from copying the design. Transfer of most cultural information from brains to artificial media increases the differences between cultural and biological information.

scholarly journals How culture and biology interact to shape language and the language faculty

2018 ◽  
Author(s):  
Kenny Smith
Keyword(s):  
Language Learning ◽  
Cultural Evolution ◽  
Cognitive Biases ◽  
Biological Evolution ◽  
Evolutionary Process ◽  
Evolutionary Models ◽  
Language Faculty ◽  
Repeated Cycle ◽  
Individual Level ◽  
Precise Relationship

Recent work suggests that linguistic structure develops through cultural evolution, as a consequence of the repeated cycle of learning and use by which languages persist. This work has important implications for our understanding of the evolution of the cognitive basis for language: in particular, human language and the cognitive capacities underpinning it are likely to have been shaped by co-evolutionary processes, where the cultural evolution of linguistic systems is shaped by and in turn shapes the biological evolution of the capacities underpinning language learning. I review several models of this co-evolutionary process, which suggest that the precise relationship between evolved biases in individuals and the structure of linguistic systems depends on the extent to which cultural evolution masks or unmasks individual-level cognitive biases from selection. I finish by discussing how these co-evolutionary models might be extended to cases where the biases involved in learning are themselves shaped by experience, as is the case for language.

Contrasting tactical and strategic dynamics on a Clausewitz landscape

2019 ◽  
Vol 17 (2) ◽  
pp. 143-153
Author(s):  
Rodrick Wallace
Keyword(s):  
Statistical Models ◽  
Limit Theorems ◽  
Large Scale ◽  
Evolutionary Process ◽  
Short Term ◽  
Local Resources ◽  
Human Organization ◽  
The World ◽  
Short Time

Statistical models based on the asymptotic limit theorems of control and information theories allow formal examination of the essential differences between short-time “tactical” confrontations and a long-term “strategic” conflict dominated by evolutionary process. The world of extended coevolutionary conflict is not the world of sequential “muddling through.” The existential strategic challenge is to take cognitive control of a long-term dynamic in which one may, in fact, be “losing” most short-term confrontations. Winning individual battles can be a relatively direct, if not simple or easy, matter of sufficient local resources, training, and resolve. Winning extended conflicts is not direct, and requires management of subtle coevolutionary phenomena subject to a dismaying punctuated equilibrium more familiar from evolutionary theory than military doctrine. Directed evolution has given us the agricultural base needed for large-scale human organization. Directed coevolution of the inevitable conflicts between the various segments of that organization may be needed for its long-term persistence.

scholarly journals HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

2019 ◽  
Vol 37 (1) ◽  
pp. 295-299 ◽  
Author(s):  
Sergei L Kosakovsky Pond ◽  
Art F Y Poon ◽  
Ryan Velazquez ◽  
Steven Weaver ◽  
N Lance Hepler ◽  
...  
Keyword(s):  
Parameter Estimation ◽  
Natural Selection ◽  
Hypothesis Testing ◽  
Statistical Tests ◽  
Evolutionary Process ◽  
Evolutionary Models ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Statistical Framework

Abstract HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting a broad range of evolutionary models to multiple sequence alignments, and for conducting subsequent parameter estimation and hypothesis testing, primarily in the maximum likelihood statistical framework. It has become a popular choice for characterizing various aspects of the evolutionary process: natural selection, evolutionary rates, recombination, and coevolution. The 2.5 release (available from www.hyphy.org) includes a completely re-engineered computational core and analysis library that introduces new classes of evolutionary models and statistical tests, delivers substantial performance and stability enhancements, improves usability, streamlines end-to-end analysis workflows, makes it easier to develop custom analyses, and is mostly backward compatible with previous HyPhy releases.

scholarly journals P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Takuma Nishimaki ◽  
Keiko Sato
Keyword(s):  
Phylogenetic Analysis ◽  
Web Application ◽  
Sequence Data ◽  
Genetic Difference ◽  
Evolutionary Process ◽  
Genetic Differences ◽  
Amino Acid Sequences ◽  
Evolutionary Information ◽  
Evolutionary Models ◽  
Link Type

Abstract Background Phylogenetic analysis strongly depends on evolutionary models. Most evolutionary models for estimating genetic differences and phylogenetic relationships do not treat gap sites in the alignment of sequences. Appropriately incorporating evolutionary information of sites containing insertions and deletions into genetic difference measures will be improve the accuracy of phylogenetic estimates. Results We introduced a new measure for estimating genetic differences, and presented P*R*O*P, a web application for performing phylogenetic analysis based on genetic difference considering the effect of gaps. As an example of phylogenetic analysis using P*R*O*P, we used complete p53 amino acid sequences of 31 organisms and illustrated that the genetic differences with and without information on sites containing gaps result in trees with different topologies. Conclusions P*R*O*P is available at https://www.rs.tus.ac.jp/bioinformatics/prop and the user can perform phylogenetic analysis by uploading sequence data on the website. The most distinctive feature of P*R*O*P is its genetic difference that is estimated without eliminating gap sites for alignment sequences, which helps users detect meaningful difference in an evolutionary process. The source code is available in GitHub: https://github.com/TUS-Satolab/PROP.

scholarly journals La evolución de técnicas y fenómenos: hacia una explicación de la "confección" del mundo

1996 ◽  
Vol 28 (82) ◽  
pp. 25-66
Author(s):  
Sergio F. Martínez ◽  
Edna Suárez
Keyword(s):  
Population Biology ◽  
Evolutionary Process ◽  
Evolutionary Model ◽  
Nucleic Acid Hybridization ◽  
Experimental Techniques ◽  
Scientific Change ◽  
Causal Process ◽  
Evolutionary Models ◽  
The World ◽  
Common Objection

In recent articles some authors (e.g. Pickering 1989, Hacking 1992) have pointed out a process of gradual adjustment or tailoring between phenomena, models and experimental techniques. However, the whole idea of tailoring or adjusting has been dealt with as a mere metaphore. In this paper we present an evolutionary model of phenomena and techniques which explains this gradual adjustment or tailoring as an adaptative causal process, i.e. not as a mere metaphor. Our aim is accomplished in three steps. First, we arrive at the general conditions that changes in a population of entities with reproductive capabilities have to satisfy in order to be modelled as an evolutionary process, in a causal-explanatory sense. We show that a characterization of the class of experimental techniques (a class associated with an experimental tradition) meet these conditions, and we examine in detail how the nucleic acid hybridization techniques used in molecular biology can be modelled in the way we propose. A second step is to show that the sort of variability that metters in evolutionary models of techniques and phenomena is aggregative variability, i.e. the sort of variability that can be selected. This is an important point, since most evolutionary models of technical and scientific change in the literature fail to satisfy this requirement. A common objection to evolutionary models of scientific change is that fitness, the central notion of evolutionary models in population biology, has no counterpart in these models. We show that our model can provide a natural concept of fitness, a concept that has a similar role to play in our model as in biological models. Finally, as a third step, we conclude with an explanation of how the world can be said to be tailored. It is the result of an evolutionary process which incorporates inextricably related conceptual and material resources. In this sense, the world consists of phenomena that are made by us, but which are not mere inventions of our mind.

scholarly journals Your place or mine? A phylogenetic comparative analysis of marital residence in Indo-European and Austronesian societies

2010 ◽  
Vol 365 (1559) ◽  
pp. 3913-3922 ◽  
Author(s):  
Laura Fortunato ◽  
Fiona Jordan
Keyword(s):  
Cultural Change ◽  
Large Scale ◽  
Comparative Method ◽  
Phylogenetic Comparative Methods ◽  
Systematic Testing ◽  
Common Features ◽  
Alternative Hypotheses ◽  
Ethnographic Data ◽  
Tree Building ◽  
Explicit Criteria

Accurate reconstruction of prehistoric social organization is important if we are to put together satisfactory multidisciplinary scenarios about, for example, the dispersal of human groups. Such considerations apply in the case of Indo-European and Austronesian, two large-scale language families that are thought to represent Neolithic expansions. Ancestral kinship patterns have mostly been inferred through reconstruction of kin terminologies in ancestral proto-languages using the linguistic comparative method, and through geographical or distributional arguments based on the comparative patterns of kin terms and ethnographic kinship ‘facts’. While these approaches are detailed and valuable, the processes through which conclusions have been drawn from the data fail to provide explicit criteria for systematic testing of alternative hypotheses. Here, we use language trees derived using phylogenetic tree-building techniques on Indo-European and Austronesian vocabulary data. With these trees, ethnographic data and Bayesian phylogenetic comparative methods, we statistically reconstruct past marital residence and infer rates of cultural change between different residence forms, showing Proto-Indo-European to be virilocal and Proto-Malayo-Polynesian uxorilocal. The instability of uxorilocality and the rare loss of virilocality once gained emerge as common features of both families.

scholarly journals Trait Evolution with Jumps: Illusionary Normality

2017 ◽  
Author(s):  
Krzysztof Bartoszek
Keyword(s):  
Stochastic Process ◽  
Weak Convergence ◽  
Comparative Methods ◽  
The Other ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Models ◽  
Trait Evolution ◽  
Other Hand ◽  
Extinction Component

ABSTRACTPhylogenetic comparative methods for real-valued traits usually make use of stochastic process whose trajectories are continuous. This is despite biological intuition that evolution is rather punctuated than gradual. On the other hand, there has been a number of recent proposals of evolutionary models with jump components. However, as we are only beginning to understand the behaviour of branching Ornstein–Uhlenbeck (OU) processes the asymptotics of branching OU processes with jumps is an even greater unknown. In this work we build up on a previous study concerning OU with jumps evolution on a pure birth tree. We introduce an extinction component and explore via simulations, its effects on the weak convergence of such a process. We furthermore, also use this work to illustrate the simulation and graphic generation possibilities of the mvSLOUCH package.

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