scholarly journals Information geometry for phylogenetic trees

2021 ◽  
Vol 82 (3) ◽  
Author(s):  
M. K. Garba ◽  
T. M. W. Nye ◽  
J. Lueg ◽  
S. F. Huckemann
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Covariance Matrices ◽  
Affine Invariant ◽  
Leibler Divergence ◽  
Fisher Information Metric ◽  
Gradient Descent Algorithm ◽  
Information Metric ◽  
Point Set ◽  
New Space

AbstractWe propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than existing spaces: in wald space, trees are close if they induce similar distributions on genetic sequence data. As a point set, wald space contains the previously developed Billera–Holmes–Vogtmann (BHV) tree space; it also contains disconnected forests, like the edge-product (EP) space but without certain singularities of the EP space. We investigate two related geometries on wald space. The first is the geometry of the Fisher information metric of character distributions induced by the two-state symmetric Markov substitution process on each tree. Infinitesimally, the metric is proportional to the Kullback–Leibler divergence, or equivalently, as we show, to any f-divergence. The second geometry is obtained analogously but using a related continuous-valued Gaussian process on each tree, and it can be viewed as the trace metric of the affine-invariant metric for covariance matrices. We derive a gradient descent algorithm to project from the ambient space of covariance matrices to wald space. For both geometries we derive computational methods to compute geodesics in polynomial time and show numerically that the two information geometries (discrete and continuous) are very similar. In particular, geodesics are approximated extrinsically. Comparison with the BHV geometry shows that our canonical and biologically motivated space is substantially different.

Information geometry of divergence functions

2010 ◽  
Vol 58 (1) ◽  
pp. 183-195 ◽  
Author(s):  
S. Amari ◽  
A. Cichocki
Keyword(s):  
Probability Distributions ◽  
Flat Space ◽  
Information Geometry ◽  
Dual Pair ◽  
Bregman Divergence ◽  
Bregman Divergences ◽  
Leibler Divergence ◽  
Fisher Information Metric ◽  
Information Metric ◽  
Dually Flat Space

Information geometry of divergence functionsMeasures of divergence between two points play a key role in many engineering problems. One such measure is a distance function, but there are many important measures which do not satisfy the properties of the distance. The Bregman divergence, Kullback-Leibler divergence andf-divergence are such measures. In the present article, we study the differential-geometrical structure of a manifold induced by a divergence function. It consists of a Riemannian metric, and a pair of dually coupled affine connections, which are studied in information geometry. The class of Bregman divergences are characterized by a dually flat structure, which is originated from the Legendre duality. A dually flat space admits a generalized Pythagorean theorem. The class off-divergences, defined on a manifold of probability distributions, is characterized by information monotonicity, and the Kullback-Leibler divergence belongs to the intersection of both classes. Thef-divergence always gives the α-geometry, which consists of the Fisher information metric and a dual pair of ±α-connections. The α-divergence is a special class off-divergences. This is unique, sitting at the intersection of thef-divergence and Bregman divergence classes in a manifold of positive measures. The geometry derived from the Tsallisq-entropy and related divergences are also addressed.

Population genetics, phylogeography, and systematics of the thornyhead rockfishes (Sebastolobus) along the deep continental slopes of the North Pacific Ocean

2000 ◽  
Vol 57 (8) ◽  
pp. 1701-1717 ◽  
Author(s):  
Carol A Stepien ◽  
Alison K Dillon ◽  
Amy K Patterson
Keyword(s):  
Pacific Ocean ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
North Pacific Ocean ◽  
Geographic Distance ◽  
The North ◽  
Continental Slopes ◽  
Genetic Patterns ◽  
Northern Pacific ◽  
Shortspine Thornyhead

Population genetic, phylogeographic, and systematic relationships are elucidated among the three species comprising the thornyhead rockfish genus Sebastolobus (Teleostei: Scorpaenidae). Genetic variation among sampling sites representing their extensive ranges along the deep continental slopes of the northern Pacific Ocean is compared using sequence data from the left domain of the mtDNA control region. Comparisons are made among the shortspine thornyhead (S. alascanus) (from seven locations), the longspine thornyhead (S. altivelis) (from five sites), which are sympatric in the northeast, and the broadbanded thornyhead (S. macrochir) (a single site) from the northwest. Phylogenetic trees rooted to Sebastes show that S. macrochir is the sister taxon of S. alascanus and S. altivelis. Intraspecific genetic variability is appreciable, with most individuals having unique haplotypes. Gene flow is substantial among some locations and others diverged significantly. Genetic divergences among sampling sites for S. alascanus indicate an isolation by geographic distance pattern. Genetic divergences for S. altivelis are unrelated to the hypothesis of isolation by geographic distance and appear to be more consistent with the hypothesis of larval retention in currents and gyres. Differences in geographic genetic patterns between the species are attributed to life history differences in their relative mobilities as juveniles and adults.

scholarly journals Origin of the European avian-like swine influenza viruses

2014 ◽  
Vol 95 (11) ◽  
pp. 2372-2376 ◽  
Author(s):  
Andi Krumbholz ◽  
Jeannette Lange ◽  
Andreas Sauerbrei ◽  
Marco Groth ◽  
Matthias Platzer ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Swine Influenza ◽  
H1n1 Influenza ◽  
Molecular Data ◽  
Influenza Viruses ◽  
Time Resolved ◽  
Genotype Constellation ◽  
Tree Inference

The avian-like swine influenza viruses emerged in 1979 in Belgium and Germany. Thereafter, they spread through many European swine-producing countries, replaced the circulating classical swine H1N1 influenza viruses, and became endemic. Serological and subsequent molecular data indicated an avian source, but details remained obscure due to a lack of relevant avian influenza virus sequence data. Here, the origin of the European avian-like swine influenza viruses was analysed using a collection of 16 European swine H1N1 influenza viruses sampled in 1979–1981 in Germany, the Netherlands, Belgium, Italy and France, as well as several contemporaneous avian influenza viruses of various serotypes. The phylogenetic trees suggested a triple reassortant with a unique genotype constellation. Time-resolved maximum clade credibility trees indicated times to the most recent common ancestors of 34–46 years (before 2008) depending on the RNA segment and the method of tree inference.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

Phylogenomics of orchids and their mycorrhizal fungi : trees, diversity, and the pursuit of symbiosis

2019 ◽  
Author(s):  
◽  
Sarah Unruh
Keyword(s):  
Mycorrhizal Fungi ◽  
Phylogenetic Trees ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Mycorrhizal Symbiosis ◽  
Sequencing Data ◽  
Phylogenetic Structure ◽  
University Of Missouri ◽  
Fungal Symbiosis

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Phylogenetic trees show us how organisms are related and provide frameworks for studying and testing evolutionary hypotheses. To better understand the evolution of orchids and their mycorrhizal fungi, I used high-throughput sequencing data and bioinformatic analyses, to build phylogenetic hypotheses. In Chapter 2, I used transcriptome sequences to both build a phylogeny of the slipper orchid genera and to confirm the placement of a polyploidy event at the base of the orchid family. Polyploidy is hypothesized to be a strong driver of evolution and a source of unique traits so confirming this event leads us closer to explaining extant orchid diversity. The list of orthologous genes generated from this study will provide a less expensive and more powerful method for researchers examining the evolutionary relationships in Orchidaceae. In Chapter 3, I generated genomic sequence data for 32 fungal isolates that were collected from orchids across North America. I inferred the first multi-locus nuclear phylogenetic tree for these fungal clades. The phylogenetic structure of these fungi will improve the taxonomy of these clades by providing evidence for new species and for revising problematic species designations. A robust taxonomy is necessary for studying the role of fungi in the orchid mycorrhizal symbiosis. In chapter 4 I summarize my work and outline the future directions of my lab at Illinois College including addressing the remaining aims of my Community Sequencing Proposal with the Joint Genome Institute by analyzing the 15 fungal reference genomes I generated during my PhD. Together these chapters are the start of a life-long research project into the evolution and function of the orchid/fungal symbiosis.

scholarly journals Distribution of Viable Bacteria in the Dust-Generating Natural Source Area of the Gobi Region, Mongolia

Atmosphere ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 893
Author(s):  
Katsuro Hagiwara ◽  
Tamaki Matsumoto ◽  
Purevsuren Tsedendamba ◽  
Kenji Baba ◽  
Buho Hoshino
Keyword(s):  
Phylogenetic Trees ◽  
Surface Soil ◽  
Sequence Data ◽  
Source Area ◽  
Soil Surface ◽  
Genetic Identification ◽  
Gobi Desert ◽  
Health Concept ◽  
Dry Lake ◽  
Live Bacteria

The Gobi Desert is a major source of dust events, whose frequency of occurrence and damage caused have recently significantly increased. In the present study, we investigated the types of live bacteria present in the surface soil of the Gobi Desert in Mongolia, and determined their genetic identification as well as their geographical distribution. During the survey, four different topographies (dry lake bed, wadi, well, and desert steppe) were selected, and land characteristics were monitored for moisture and temperature. The surface soil was aerobically cultured to isolate bacterial colonies, and their 16s rDNA regions were sequenced. The sequence data were identified through NCBI-BLAST analysis and generated phylogenetic trees. The results revealed two phyla and seven families of isolates from the sample points. Each isolate was characterized by their corresponding sample site. The characteristics of land use and soil surface bacteria were compared. Most of the bacteria originated from the soil, however, animal-derived bacteria were also confirmed in areas used by animals. Our findings confirmed the existence of live bacteria in the dust-generating area, suggesting that their presence could affect animal and human health. Therefore, it is necessary to further investigate dust microbes based on the One Health concept.

scholarly journals Evolution of pollination syndromes and corolla symmetry in Balsaminaceae reconstructed using phylogenetic comparative analyses

2020 ◽  
Author(s):  
Saroj Ruchisansakun ◽  
Arne Mertens ◽  
Steven B Janssens ◽  
Erik F Smets ◽  
Timotheüs van der Niet
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Plastid Dna ◽  
Pollination Syndrome ◽  
Pollination Syndromes ◽  
Bee Pollination ◽  
Floral Symmetry ◽  
Considerable Uncertainty ◽  
Pollination Systems

Abstract Background and Aims Floral diversity as a result of plant–pollinator interactions can evolve by two distinct processes: shifts between pollination systems or divergent use of the same pollinator. Although both are pollinator driven, the mode, relative importance and interdependence of these different processes are rarely studied simultaneously. Here we apply a phylogenetic approach using the Balsaminaceae (including the species-rich genus Impatiens) to simultaneously quantify shifts in pollination syndromes (as inferred from the shape and colour of the perianth), as well as divergent use of the same pollinator (inferred from corolla symmetry). Methods For 282 species we coded pollination syndromes based on associations between floral traits and known pollination systems, and assessed corolla symmetry. The evolution of these traits was reconstructed using parsimony- and model-based approaches, using phylogenetic trees derived from phylogenetic analyses of nuclear ribosomal and plastid DNA sequence data. Key Results A total of 71 % of studied species have a bee pollination syndrome, 22 % a bimodal syndrome (Lepidoptera and bees), 3 % a bird pollination syndrome and 5 % a syndrome of autogamy, while 19 % of species have an asymmetrical corolla. Although floral symmetry and pollination syndromes are both evolutionarily labile, the latter shifts more frequently. Shifts in floral symmetry occurred mainly in the direction towards asymmetry, but there was considerable uncertainty in the pattern of shift direction for pollination syndrome. Shifts towards asymmetrical flowers were associated with a bee pollination syndrome. Conclusion Floral evolution in Impatiens has occurred through both pollination syndrome shifts and divergent use of the same pollinator. Although the former appears more frequent, the latter is likely to be underestimated. Shifts in floral symmetry and pollination syndromes depend on each other but also partly on the region in which these shifts take place, suggesting that the occurrence of pollinator-driven evolution may be determined by the availability of pollinator species at large geographical scales.

scholarly journals Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

2020 ◽  
Vol 117 (29) ◽  
pp. 17104-17111
Author(s):  
Nicola F. Müller ◽  
Ugnė Stolz ◽  
Gytis Dudas ◽  
Tanja Stadler ◽  
Timothy G. Vaughan
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Population Level ◽  
Influenza Viruses ◽  
Monte Carlo Algorithm ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Human Influenza ◽  
Fitness Benefits

Reassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. Here, we introduce a coalescent-based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. This algorithm provides the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full-genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses.

scholarly journals Two new Chrysomyxa rust species on the endemic plant, Picea asperata in western China, and expanded description of C. succinea

Phytotaxa ◽  
2017 ◽  
Vol 292 (3) ◽  
pp. 218 ◽  
Author(s):  
JING CAO ◽  
CHENGMING TIAN ◽  
YINGMEI LIANG ◽  
CHONGJUAN YOU
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Morphological Characters ◽  
Western China ◽  
Endemic Plant ◽  
Internal Transcribed Spacer Region ◽  
Dna Sequence Data ◽  
Species Cluster ◽  
Picea Asperata ◽  
First Time

Two new rust species, Chrysomyxa diebuensis and C. zhuoniensis, on Picea asperata are recognized by morphological characters and DNA sequence data. A detailed description, illustrations, and discussion concerning morphologically similar and phylogenetically closely related species are provided for each species. From light and scanning electron microscopy observations C. diebuensis is characterized by the nailhead to peltate aeciospores, with separated stilt-like base. C. zhuoniensis differs from other known Chrysomyxa species in the annulate aeciospores with distinct longitudinal smooth cap at ends of spores, as well as with a broken, fissured edge. Analysis based on internal transcribed spacer region (ITS) partial gene sequences reveals that the two species cluster as a highly supported group in the phylogenetic trees. Correlations between the morphological and phylogenetic features are discussed. Illustrations and a detailed description are also provided for the aecia of C. succinea in China for the first time.

Morphology and molecular studies on large Neidium species (Bacillariophyta) of North America, including an examination of Ehrenberg’s types

Phytotaxa ◽  
2015 ◽  
Vol 220 (3) ◽  
pp. 201 ◽  
Author(s):  
Keely E Lefebvre ◽  
Paul B Hamilton
Keyword(s):  
New York ◽  
North America ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
New York State ◽  
Central Area ◽  
Large Species ◽  
Sem Images ◽  
Wide Range ◽  
Future Work

The genus Neidium contains a large array of diatoms with a wide range in structural and morphological forms. Many of the larger species in this genus are old taxa dating back to the 1800s. However, there continues to be confusion over these large species including N. iridis, N. dilatatum, N. firma, and N. amphigomphus. In this study, selected Neidium taxa from North America were examined using LM and SEM images from both Ehrenberg’s original samples and present day samples from Ontario (Canada) and New York State (USA). As well, Neidium individuals were isolated from Adriondack Park, NY (USA) and Ontario (Canada), amplified using a nested PCR protocol and sequenced for rbcL and 18S barcoding genes. The sequence data was concatenated to construct phylogenetic trees using Maximum Likelihood and Bayesian Analysis techniques. Here we present emended species descriptions and sequence data of four previously named Neidium taxa: N. tumescens, N. hitchcockii, N. dilatatum and N. amphigomphus. In addition, we designate isolectotypes for N. hitchcockii, N. dilatatum and N. amphigomphus. A new species is also formally described—N. fossum, sp. nov.—with a designated holotype and sequence data. Neidium fossum is distinguished by its size, longitudinal canal structure, central area and proximal raphe ends. Future work combining traditional morphological methods and phylogenetic methods will allow for further delineation of Neidium species and other diatom taxa.

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