scholarly journals SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

2011 ◽  
Vol 27 (20) ◽  
pp. 2910-2912 ◽  
Author(s):  
F. Bielejec ◽  
A. Rambaut ◽  
M. A. Suchard ◽  
P. Lemey
Keyword(s):  
Evolutionary Dynamics ◽  
Phylogenetic Reconstruction

DISTANCE-BASED PHYLOGENETIC ALGORITHMS: NEW INSIGHTS AND APPLICATIONS

2010 ◽  
Vol 20 (supp01) ◽  
pp. 1511-1532 ◽  
Author(s):  
S. POMPEI ◽  
E. CAGLIOTI ◽  
V. LORETO ◽  
F. TRIA
Keyword(s):  
Horizontal Transfer ◽  
Evolutionary Dynamics ◽  
Phylogenetic Reconstruction ◽  
Local Property ◽  
Reconstruction Algorithms ◽  
Reconstruction Methods ◽  
Tree Length ◽  
Point Condition ◽  
Generative Algorithms ◽  
The One

Phylogenetic methods have recently been rediscovered in several interesting areas among which immunodynamics, epidemiology and many branches of evolutionary dynamics. In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence, a divergence arises between the true evolutionary distances and the distances between pairs of taxa as inferred from the available data, making the phylogenetic reconstruction a challenging problem. Mathematically this divergence translates in the non-additivity of the actual distances between taxa and the quest for new algorithms able to efficiently cope with these effects is wide open. In distance-based reconstruction methods, two properties of additive distances were extensively exploited as antagonist criteria to drive phylogeny reconstruction: on the one hand a local property of quartets, i.e. sets of four taxa in a tree, the four-point condition; on the other hand, a recently proposed formula that allows to write the tree length as a function of the distances between taxa, the Pauplin's formula. A deeper comprehension of the effects of the non-additivity on the inspiring principles of the existing reconstruction algorithms is thus of paramount importance. In this paper we present a comparative analysis of the performances of the most important distance-based phylogenetic algorithms. We focus in particular on the dependence of their performances on two main sources of non-additivity: back-mutation processes and horizontal transfer processes. The comparison is carried out in the framework of a set of generative algorithms for phylogenies that incorporate non-additivity in a tunable way.

scholarly journals On Subtrees of Fan Graphs, Wheel Graphs, and “Partitions” of Wheel Graphs under Dynamic Evolution

Mathematics ◽  
2019 ◽  
Vol 7 (5) ◽  
pp. 472 ◽  
Author(s):  
Yu Yang ◽  
An Wang ◽  
Hua Wang ◽  
Wei-Ting Zhao ◽  
Dao-Qiang Sun
Keyword(s):  
Evolutionary Dynamics ◽  
Phylogenetic Reconstruction ◽  
Extremal Problems ◽  
Dynamic Evolution ◽  
Graph Invariants ◽  
Wheel Graphs

The number of subtrees, or simply the subtree number, is one of the most studied counting-based graph invariants that has applications in many interdisciplinary fields such as phylogenetic reconstruction. Motivated from the study of graph surgeries on evolutionary dynamics, we consider the subtree problems of fan graphs, wheel graphs, and the class of graphs obtained from “partitioning” wheel graphs under dynamic evolution. The enumeration of these subtree numbers is done through the so-called subtree generation functions of graphs. With the enumerative result, we briefly explore the extremal problems in the corresponding class of graphs. Some interesting observations on the behavior of the subtree number are also presented.

scholarly journals Cancer phylogenetics using single-cell RNA-seq data

2021 ◽  
Author(s):  
Jiri C. Moravec ◽  
Robert Lanfear ◽  
David Spector ◽  
Sarah Diermeier ◽  
Alex Gavryushkin
Keyword(s):  
Single Cell ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Computational Cost ◽  
Phylogenetic Reconstruction ◽  
Single Nucleotide Variants ◽  
Expression Levels ◽  
Full Picture ◽  
Structure Heterogeneity ◽  
Differential Gene

Phylogenetic methods are emerging as an useful tool to understand cancer evolutionary dynamics, including tumor structure, heterogeneity, and progression. Most currently used approaches utilize either bulk whole genome sequencing (WGS) or single-cell DNA sequencing (scDNA-seq) and are based on calling copy number alterations and single nucleotide variants (SNVs). Here we explore the potential of single-cell RNA sequencing (scRNA-seq) to reconstruct cancer evolutionary dynamics. scRNA-seq is commonly applied to explore differential gene expression of cancer cells throughout tumor progression. The method exacerbates the single-cell sequencing problem of low yield per cell with uneven expression levels. This accounts for low and uneven sequencing coverage and makes SNV detection and phylogenetic analysis challenging. In this paper, we demonstrate for the first time that scRNA-seq data contains sufficient evolutionary signal and can be utilized in phylogenetic analyses. We explore and compare results of such analyses based on both expression levels and SNVs called from our scRNA-seq data. Both techniques are shown to be useful for reconstructing phylogenetic relationships between cells, reflecting the clonal composition of a tumor. Without an explicit error model, standardized expression values appears to be more powerful and informative than the SNV values at a lower computational cost, due to being a by-product of standard expression analysis. Our results suggest that scRNA-seq can be a competitive alternative or useful addition to conventional scDNA-seq phylogenetic reconstruction. Our results open up a new direction of somatic phylogenetics based on scRNA-seq data. Further research is required to refine and improve these approaches to capture the full picture of somatic evolutionary dynamics in cancer.

scholarly journals Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales

2020 ◽  
Vol 6 (11) ◽  
Author(s):  
Henry Secaira-Morocho ◽  
José A. Castillo ◽  
Adam Driks
Keyword(s):  
Environmental Conditions ◽  
Evolutionary Dynamics ◽  
Sequence Similarity ◽  
Phylogenetic Reconstruction ◽  
Purifying Selection ◽  
Spore Coat ◽  
Coat Proteins ◽  
Content Type ◽  
Link Type ◽  
Spore Coat Proteins

Among members of the Bacillales order, there are several species capable of forming a structure called an endospore. Endospores enable bacteria to survive under unfavourable growth conditions and germinate when environmental conditions are favourable again. Spore-coat proteins are found in a multilayered proteinaceous structure encasing the spore core and the cortex. They are involved in coat assembly, cortex synthesis and germination. Here, we aimed to determine the diversity and evolutionary processes that have influenced spore-coat genes in various spore-forming species of Bacillales using an in silico approach. For this, we used sequence similarity searching algorithms to determine the diversity of coat genes across 161 genomes of Bacillales. The results suggest that among Bacillales, there is a well-conserved core genome, composed mainly by morphogenetic coat proteins and spore-coat proteins involved in germination. However, some spore-coat proteins are taxa-specific. The best-conserved genes among different species may promote adaptation to changeable environmental conditions. Because most of the Bacillus species harbour complete or almost complete sets of spore-coat genes, we focused on this genus in greater depth. Phylogenetic reconstruction revealed eight monophyletic groups in the Bacillus genus, of which three are newly discovered. We estimated the selection pressures acting over spore-coat genes in these monophyletic groups using classical and modern approaches and detected horizontal gene transfer (HGT) events, which have been further confirmed by scanning the genomes to find traces of insertion sequences. Although most of the genes are under purifying selection, there are several cases with individual sites evolving under positive selection. Finally, the HGT results confirm that sporulation is an ancestral feature in Bacillus .

scholarly journals Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5573 ◽  
Author(s):  
Artur Burzyński ◽  
Marianna Soroka
Keyword(s):  
Evolutionary Dynamics ◽  
Phylogenetic Reconstruction ◽  
Real Problem ◽  
Data Sets ◽  
Long Branch Attraction ◽  
The Family ◽  
Complete Sequences ◽  
First Time ◽  
Unio Pictorum ◽  
Sinanodonta Woodiana

Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.

scholarly journals Geospatial distributions reflect temperatures of linguistic features

2021 ◽  
Vol 7 (1) ◽  
pp. eabe6540
Author(s):  
Henri Kauhanen ◽  
Deepthi Gopal ◽  
Tobias Galla ◽  
Ricardo Bermúdez-Otero
Keyword(s):  
Stochastic Process ◽  
Longitudinal Data ◽  
Language Change ◽  
Evolutionary Dynamics ◽  
Phylogenetic Reconstruction ◽  
Historical Evolution ◽  
Linguistic Features ◽  
Linguistic Change ◽  
Linguistic Feature ◽  
Vertical Descent

Quantifying the speed of linguistic change is challenging because the historical evolution of languages is sparsely documented. Consequently, traditional methods rely on phylogenetic reconstruction. Here, we propose a model-based approach to the problem through the analysis of language change as a stochastic process combining vertical descent, spatial interactions, and mutations in both dimensions. A notion of linguistic temperature emerges naturally from this analysis as a dimensionless measure of the propensity of a linguistic feature to undergo change. We demonstrate how temperatures of linguistic features can be inferred from their present-day geospatial distributions, without recourse to information about their phylogenies. Thus, the evolutionary dynamics of language, operating across thousands of years, leave a measurable geospatial signature. This signature licenses inferences about the historical evolution of languages even in the absence of longitudinal data.

A new species of Contomastix (Squamata, Teiidae) supported by total evidence, with remarks on diagnostic characters defining the genus

2019 ◽  
pp. 23-36
Author(s):  
Mario. R. Cabrera
Keyword(s):  
New Species ◽  
Geographic Distribution ◽  
Phylogenetic Reconstruction ◽  
Total Evidence ◽  
Molecular Evidence ◽  
Proximal Margin ◽  
Diagnostic Characters ◽  
Morphological Differences ◽  
A New Species ◽  
Molecular Characters

Formerly Cnemidophorus was thought to be the most speciose genus of Teiidae. This genus comprised four morphological groups that were later defined as four different genera, Ameivula, Aurivela, Cnemidophorus and Contomastix. The last appears as paraphyletic in a recent phylogenetic reconstruction based on morphology, but monophyletic in a reconstruction using molecular characters. Six species are allocated to Contomastix. One of them, C. lacertoides, having an extensive and disjunct geographic distribution in Argentina, Uruguay and Brazil. Preliminary analyses revealed morphological differences among its populations, suggesting that it is actually a complex of species. Here, we describe a new species corresponding to the Argentinian populations hitherto regarded as C. lacertoides, by integrating morphological and molecular evidence. Furthermore, we demonstrate that the presence of notched proximal margin of the tongue is a character that defines the genus Contomastix.

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