RNA-Based Phylogenetic Methods

2005 ◽  
pp. 191-210
Author(s):  
Magnus Rattray ◽  
Paul G. Higgs
Keyword(s):  
Phylogenetic Methods

scholarly journals Novel metric for hyperbolic phylogenetic tree embeddings

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Hirotaka Matsumoto ◽  
Takahiro Mimori ◽  
Tsukasa Fukunaga
Keyword(s):  
Phylogenetic Tree ◽  
Hyperbolic Space ◽  
Nearest Neighbor ◽  
Cancer Genomics ◽  
Geometric Approach ◽  
Artificial Intelligence Research ◽  
Phylogenetic Methods ◽  
Novel Approach ◽  
Multiple Trees ◽  
Euclidean Embeddings

Abstract Advances in experimental technologies, such as DNA sequencing, have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. Furthermore, we proposed a novel approach based on our metric to integrate multiple trees for analyzing tree nodes or imputing missing distances. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods.

A 10-gene phylogeny ofSolanumsectionHerpystichum(Solanaceae) and a comparison of phylogenetic methods

2011 ◽  
Vol 98 (8) ◽  
pp. 1356-1365 ◽  
Author(s):  
Eric J. Tepe ◽  
Frank T. Farruggia ◽  
Lynn Bohs
Keyword(s):  
Gene Phylogeny ◽  
Phylogenetic Methods

Performance of Phylogenetic Methods in Simulation

1995 ◽  
Vol 44 (1) ◽  
pp. 17-48 ◽  
Author(s):  
John P. Huelsenbeck
Keyword(s):  
Phylogenetic Methods

scholarly journals The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses among Paediatric Cases in Sydney, Australia.

2020 ◽  
Author(s):  
Dillon Adam ◽  
Xin Chen ◽  
Matthew Scotch ◽  
C. Raina MacIntyre ◽  
Dominic Dwyer ◽  
...  
Keyword(s):  
Disease Severity ◽  
Respiratory Tract Infections ◽  
Clinical Symptoms ◽  
Age Groups ◽  
Epidemiological Evidence ◽  
Treatment Practices ◽  
Phylogenetic Methods ◽  
Significant Burden ◽  
Tract Infections ◽  
Sydney Australia

Background Rhinoviruses (RV) represent the most common aetiological agent of all acute respiratory tract infections across all age groups and a significant burden of disease among children. Recent studies have shown that RV-A and RV-C species are associated with varying degrees of disease severity and clinical symptoms. Methods In this study, we uncovered potential associations between RV species and subtypes, and clinical disease severity using a matched dataset of 52 RV isolates sampled from children (<18 years) in Sydney, Australia between 2006 and 2009 using epidemiological and phylogenetic methods. Results We found that RV-C was significantly more likely to be isolated from paediatric cases under two years of age compared to RV-A, although no significant differences in recorded symptoms were observed. Significant phylogenetic-trait associations between age and the VP4/VP2 capsid protein phylogeny suggests age-specific variations in infectivity among subtypes might also be possible. Conclusions This study adds to the growing body of epidemiological evidence concerning RV. Improving surveillance and testing for RV, including routine whole genome sequencing may improve our understanding of the varied diseashe outcomes of RV species and subtypes. Future studies could aim to identify specific genetic markers associated with age-specific infectivity of RV which could inform treatment practices and public health surveillance of RV.

scholarly journals The Uses and Abuses of Tree Thinking in Cultural Evolution

2021 ◽  
Author(s):  
Cara Evans ◽  
Simon J. Greenhill ◽  
Joseph Watts ◽  
Johann-Mattis List ◽  
Carlos A. Botero ◽  
...  
Keyword(s):  
Best Practices ◽  
Cultural Evolution ◽  
Cross Cultural ◽  
Tree Thinking ◽  
Phylogenetic Methods ◽  
Cultural Research ◽  
Cross Cultural Research ◽  
Cultural Traits ◽  
Lines Of Evidence ◽  
Over Time

Modern phylogenetic methods are increasingly being used to address questions about macro-level patterns in cultural evolution. These methods can illuminate the unobservable histories of cultural traits and identify the evolutionary drivers of trait-change over time, but their application is not without pitfalls. Here we outline the current scope of research in cultural tree thinking, highlighting a toolkit of best practices to navigate and avoid the pitfalls and ‘abuses’ associated with their application. We emphasise two principles that support the appropriate application of phylogenetic methodologies in cross-cultural research: researchers should (1) draw on multiple lines of evidence when deciding if and which types of phylogenetic methods and models are suitable for their cross-cultural data, and (2) carefully consider how different cultural traits might have different evolutionary histories across space and time. When used appropriately phylogenetic methods can provide powerful insights into the processes of evolutionary change that have shaped the broad patterns of human history.

scholarly journals Micromorphological, anatomical and molecular study of Hedera species (Araliaceae) in Iran

2020 ◽  
Vol 63 (2) ◽  
pp. 91-101
Author(s):  
Elham Amini ◽  
Fatemeh Nasrollahi ◽  
Ali Sattarian ◽  
Mahboobeh Haji Moradkhani ◽  
Sohrab Boozarpour ◽  
...  
Keyword(s):  
North Africa ◽  
Phylogenetic Analyses ◽  
Molecular Study ◽  
Molecular Characteristics ◽  
Nrdna Its ◽  
Anticlinal Wall ◽  
Data Set ◽  
Phylogenetic Methods ◽  
Extant Species ◽  
Qualitative Characters

Hedera, with 12 extant species, is a genus of evergreen climbers native to Europe, north Africa, and south Asia. In this study, the micromorphological, anatomical structure and molecular evidences of 11 populations from two species of Hedera (H. helix and H. pastuchovii) have been considered to evaluate the relationships in Hedera. In total, seven quantitative and qualitative characters of pollen were selected and measured. Based on this study, the anticlinal wall and surface sculpturing of seed support for separation of two species of Hedera. Micromorphology of epidermis illustrated two types of epidermal cells: puzzle-shaped and polygonal cells. Using nuclear (nrDNA ITS) marker, we reconstructed phylogenetic relationships within two species of Hedera. This data set was analyzed by phylogenetic methods including Bayesian inference, maximum likelihood, and maximum parsimony. In phylogenetic analyses, all members of two species formed a well-supported clade (PP = 1; ML/BS = 100/100) and divided into two major clades (A and B). Neighbor Net diagram demonstrated separation of the studied populations. The results showed that these taxa differ in taxonomically important micromorphological, anatomical and molecular characteristics and these data provide reliable evidence for separation of these two species.

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