scholarly journals Temporal phylogenetic networks and logic programming

2006 ◽  
Vol 6 (5) ◽  
pp. 539-558 ◽  
Author(s):  
ESRA ERDEM ◽  
VLADIMIR LIFSCHITZ ◽  
DON RINGE
Keyword(s):  
Mathematical Model ◽  
Logic Programming ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Answer Set Programming ◽  
Phylogenetic Networks ◽  
Natural Languages ◽  
European Languages ◽  
History Of ◽  
Linguistic Communities

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between prehistoric linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages.

scholarly journals Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rosanne Wallin ◽  
Leo van Iersel ◽  
Steven Kelk ◽  
Leen Stougie
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Network Inference ◽  
Phylogenetic Network ◽  
Phylogenetic Networks ◽  
Network Algorithms ◽  
Running Time ◽  
Inference Algorithms ◽  
History Of ◽  
The Impact

Abstract Background Rooted phylogenetic networks are used to display complex evolutionary history involving so-called reticulation events, such as genetic recombination. Various methods have been developed to construct such networks, using for example a multiple sequence alignment or multiple phylogenetic trees as input data. Coronaviruses are known to recombine frequently, but rooted phylogenetic networks have not yet been used extensively to describe their evolutionary history. Here, we created a workflow to compare the evolutionary history of SARS-CoV-2 with other SARS-like viruses using several rooted phylogenetic network inference algorithms. This workflow includes filtering noise from sets of phylogenetic trees by contracting edges based on branch length and bootstrap support, followed by resolution of multifurcations. We explored the running times of the network inference algorithms, the impact of filtering on the properties of the produced networks, and attempted to derive biological insights regarding the evolution of SARS-CoV-2 from them. Results The network inference algorithms are capable of constructing rooted phylogenetic networks for coronavirus data, although running-time limitations require restricting such datasets to a relatively small number of taxa. Filtering generally reduces the number of reticulations in the produced networks and increases their temporal consistency. Taxon bat-SL-CoVZC45 emerges as a major and structural source of discordance in the dataset. The tested algorithms often indicate that SARS-CoV-2/RaTG13 is a tree-like clade, with possibly some reticulate activity further back in their history. A smaller number of constructed networks posit SARS-CoV-2 as a possible recombinant, although this might be a methodological artefact arising from the interaction of bat-SL-CoVZC45 discordance and the optimization criteria used. Conclusion Our results demonstrate that as part of a wider workflow and with careful attention paid to running time, rooted phylogenetic network algorithms are capable of producing plausible networks from coronavirus data. These networks partly corroborate existing theories about SARS-CoV-2, and partly produce new avenues for exploration regarding the location and significance of reticulate activity within the wider group of SARS-like viruses. Our workflow may serve as a model for pipelines in which phylogenetic network algorithms can be used to analyse different datasets and test different hypotheses.

scholarly journals Comparing the topology of phylogenetic network generators

2021 ◽  
Author(s):  
Remie Janssen ◽  
Pengyu Liu
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Random Trees ◽  
Phylogenetic Networks ◽  
Phylogeny Reconstruction ◽  
Evolutionary Analysis ◽  
Summary Statistics ◽  
History Of

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive representation of evolutionary history compared to phylogenetic trees. Stochastic processes for generating random trees or networks are important tools in evolutionary analysis, especially in phylogeny reconstruction where they can be utilized for validation or serve as priors for Bayesian methods. However, as more network generators are developed, there is a lack of discussion or comparison for different generators. To bridge this gap, we compare a set of phylogenetic network generators by profiling topological summary statistics of the generated networks over the number of reticulations and comparing the topological profiles.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

scholarly journals Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data

2019 ◽  
Vol 69 (3) ◽  
pp. 593-601 ◽  
Author(s):  
Christopher Blair ◽  
Cécile Ané
Keyword(s):  
Gene Flow ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Genomic Data ◽  
Point Of View ◽  
Phylogenetic Networks ◽  
Lineage Sorting

Abstract Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point of view, we highlight some of the strengths and limitations of phylogenetic networks and argue that tree-based inference should not be blindly abandoned in favor of networks simply because they represent more parameter rich models. Attention should be given to model selection of reticulation complexity, and the most robust conclusions regarding evolutionary history are likely obtained when combining tree- and network-based inference.

scholarly journals The promiscuous evolutionary history of the family Bromoviridae

2008 ◽  
Vol 89 (7) ◽  
pp. 1739-1747 ◽  
Author(s):  
Francisco M. Codoñer ◽  
Santiago F. Elena
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Network ◽  
Alfalfa Mosaic Virus ◽  
Taxonomic Status ◽  
Emerging Viruses ◽  
Genomic Rnas ◽  
Virus Family ◽  
Phylogenetic Methods ◽  
The Family ◽  
History Of

Recombination and segment reassortment are important contributors to the standing genetic variation of RNA viruses and are often involved in the genesis of new, emerging viruses. This study explored the role played by these two processes in the evolutionary radiation of the plant virus family Bromoviridae. The evolutionary history of this family has been explored previously using standard molecular phylogenetic methods, but incongruences have been found among the trees inferred from different gene sequences. This would not be surprising if RNA exchange was a common event, as it is well known that recombination and reassortment of genomes are poorly described by standard phylogenetic methods. In an attempt to reconcile these discrepancies, this study first explored the extent of segment reassortment and found that it was common at the origin of the bromoviruses and cucumoviruses and at least at the origin of alfalfa mosaic virus, American plum line pattern virus and citrus leaf rugose virus. Secondly, recombination analyses were performed on each of the three genomic RNAs and it was found that recombination was very common in members of the genera Bromovirus, Cucumovirus and Ilarvirus. Several cases of recombination involving species from different genera were also identified. Finally, a phylogenetic network was constructed reflecting these genetic exchanges. The network confirmed the taxonomic status of the different genera within the family, despite the phylogenetic noise introduced by genetic exchange.

Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

2020 ◽  
Vol 70 (1) ◽  
pp. 162-180
Author(s):  
Jeffrey P Rose ◽  
Cassio A P Toledo ◽  
Emily Moriarty Lemmon ◽  
Alan R Lemmon ◽  
Kenneth J Sytsma
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Plastid Genome ◽  
Incomplete Lineage Sorting ◽  
Nuclear Genome ◽  
Reticulate Evolution ◽  
Phylogenetic Networks ◽  
Flowering Plant ◽  
Lineage Sorting ◽  
History Of

Abstract Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.]

scholarly journals Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)

2018 ◽  
Vol 68 (2) ◽  
pp. 329-346 ◽  
Author(s):  
Daniel J MacGuigan ◽  
Thomas J Near
Keyword(s):  
Evolutionary History ◽  
Introgressive Hybridization ◽  
Reticulate Evolution ◽  
Phylogenetic Networks ◽  
Model Organisms ◽  
Genome Wide ◽  
Phylogenetic Resolution ◽  
History Of ◽  
Traditional Approaches ◽  
Ancient Hybridization

Abstract Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study, we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of approximately 30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression between Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.

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