scholarly journals The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1032 ◽  
Author(s):  
Yulia Vakulenko ◽  
Andrei Deviatkin ◽  
Alexander Lukashev
Keyword(s):  
Evolutionary History ◽  
Large Datasets ◽  
Sequencing Errors ◽  
Sample Bias ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
History Of ◽  
Sequence Position ◽  
Annotation Errors ◽  
Selection Of

Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.

scholarly journals Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 70 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
Nigel French
Keyword(s):  
Evolutionary History ◽  
State Of The Art ◽  
Molecular Techniques ◽  
Evolutionary Significance ◽  
Phylogenetic Structure ◽  
Bayesian Approaches ◽  
Phylogenetic Studies ◽  
Anchored Phylogenomics ◽  
History Of ◽  
Phylogenomic Analyses

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.

Diversity and preserved shell coloration patterns of Miocene Conidae (Neogastropoda) from an exposure of the Gatun Formation, Colón Province, Panama

2018 ◽  
Vol 92 (5) ◽  
pp. 804-837 ◽  
Author(s):  
Jonathan R. Hendricks
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Feeding Habits ◽  
Shell Morphology ◽  
Snail Species ◽  
Cone Snail ◽  
Phylogenetic Studies ◽  
Biogeographic History ◽  
History Of ◽  
Coloration Patterns

AbstractExtant members of the neogastropod family Conidae (cone snails) are renowned for their often dazzling shell coloration patterns and venomous feeding habits. Many cone snail species have also been described from the fossil record, but to date have been little used to understand the evolutionary history of extant clades. The cone snail fauna of the Miocene Gatun Formation of Colón Province, Panama is especially important for understanding the temporal and biogeographic history of tropical American Conidae. Intensive, focused collecting from an exposure of the lower Gatun Formation (deposited ca. 11–10 Ma) resulted in the discovery of nearly 900 specimens of Conidae. Remarkably, many of these well-preserved specimens exhibit revealed coloration patterns when exposed to ultraviolet light. The fluorescing coloration patterns were used in conjunction with other features of shell morphology to differentiate species and, in most cases, evaluate their potential relationships to members of the extant tropical American fauna. Nine species are fully described from this locality, one of which is recognized as new:Conus(Stephanoconus)woodringin. sp. At least one, and perhaps more, additional Conidae species are also present at the study locality. The diversity of this Conidae fauna is considered moderate relative to other recently analyzed tropical American fossil assemblages. The phylogenetic diversity of the assemblage, however, is noteworthy: six of the ten species can be confidently assigned to six different clades of extant Conidae, providing potentially useful calibration points for future phylogenetic studies.http://zoobank.org/8fe00c31-8f3f-4514-85af-29068e468cd3

scholarly journals Automated selection of homologs to track the evolutionary history of proteins

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Pablo Mier ◽  
Antonio J. Pérez-Pulido ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Evolutionary History ◽  
History Of ◽  
Selection Of

scholarly journals A theory about the evolutionary history of Lachnidae and comments on the results of some molecular phylogenetic studies of aphids (Hemiptera: Aphidoidea)

2015 ◽  
Vol 84 (4) ◽  
pp. 275-287 ◽  
Author(s):  
Ole E. Heie
Keyword(s):  
Evolutionary History ◽  
Sister Group ◽  
Compound Eyes ◽  
Host Alternation ◽  
Phylogenetic Studies ◽  
The Family ◽  
Molecular Phylogenetic ◽  
History Of

Abstract Several characters of the Lachnidae are discussed, and it is explained why some of them are not plesiomorphies as previously believed, but apomorphies. This applies e.g. to the absence of host alternation in the extant genera, to the short cauda and to the presence of compound eyes in the nymphs and the apterous adults. Some characters are adaptations to attention by ants or ways of feeding. It is concluded that many characters show that the family is relatively young and probably originally had host alternation of the same kind as Aphididae, which is regarded as the sister group. The results of some molecular phylogenetic studies are discussed.

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.

scholarly journals Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage

2021 ◽  
Author(s):  
Sumaira Zaman ◽  
Samuel Sledzieski ◽  
Bonnie Berger ◽  
Yi-Chieh Wu ◽  
Mukul S. Bansal
Keyword(s):  
Evolutionary History ◽  
Viral Evolution ◽  
Emerging Pathogens ◽  
Phylogenetic Methods ◽  
History Of ◽  
Tree Estimation ◽  
Phylogenetic Reconciliation ◽  
Horseshoe Bat ◽  
Insight Into ◽  
Family Trees

An accurate understanding of the evolutionary history of rapidly-evolving viruses like SARS-CoV-2, responsible for the COVID-19 pandemic, is crucial to tracking and preventing the spread of emerging pathogens. However, viruses undergo frequent recombination, which makes it difficult to trace their evolutionary history using traditional phylogenetic methods. Here, we present a phylogenetic workflow, virDTL, for analyzing viral evolution in the presence of recombination. Our approach leverages reconciliation methods developed for inferring horizontal gene transfer in prokaryotes, and, compared to existing tools, is uniquely able to identify ancestral recombinations while accounting for several sources of inference uncertainty, including in the construction of a strain tree, estimation and rooting of gene family trees, and reconciliation itself. We apply this workflow to the Sarbecovirus subgenus and demonstrate how a principled analysis of predicted recombination gives insight into the evolution of SARS-CoV-2. In addition to providing confirming evidence for the horseshoe bat as its zoonotic origin, we identify several ancestral recombination events that merit further study.

scholarly journals Recombination patterns in coronaviruses

2021 ◽  
Author(s):  
Nicola F. Müller ◽  
Kathryn E. Kistler ◽  
Trevor Bedford
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Template Switching ◽  
Recombination Rates ◽  
Genetic Sequence ◽  
Recombinant Viruses ◽  
Switching Model ◽  
Shared History ◽  
Phylogenetic Methods ◽  
History Of

AbstractAs shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption. This makes it problematic to apply phylogenetic methods to study recombining pathogens, including, for example, coronaviruses. Here, we introduce a Markov chain Monte Carlo approach that allows inference of recombination networks from genetic sequence data under a template switching model of recombination. Using this method, we first show that recombination is extremely common in the evolutionary history of SARS-like coronaviruses. We then show how recombination rates across the genome of the human seasonal coronaviruses 229E, OC43 and NL63 vary with rates of adaptation. This suggests that recombination could be beneficial to fitness of human seasonal coronaviruses. Additionally, this work sets the stage for Bayesian phylogenetic tracking of the spread and evolution of SARS-CoV-2 in the future, even as recombinant viruses become prevalent.

scholarly journals A Molecular Phylogeny of the Dove Genera Streptopelia and Columba

The Auk ◽  
2001 ◽  
Vol 118 (4) ◽  
pp. 874-887 ◽  
Author(s):  
Kevin P. Johnson ◽  
Selvino de Kort ◽  
Karen Dinwoodey ◽  
A. C. Mateman ◽  
Carel ten Cate ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
New World ◽  
Mitochondrial Gene ◽  
Base Pairs ◽  
Old World ◽  
Phylogenetic Methods ◽  
History Of ◽  
Taxonomic Changes

Abstract Evolutionary history of the dove genus Streptopelia has not been examined with rigorous phylogenetic methods. We present a study of phylogenetic relationships of Streptopelia based on over 3,600 base pairs of nuclear and mitochondrial gene sequences. To test for monophyly of Streptopelia, we used several other columbiform taxa, including Columba (Old and New World), Macropygia, Reinwardtoena, and the enigmatic Pink Pigeon (Nesoenas mayeri). On the basis of our analyses, Streptopelia (as currently defined) is not monophyletic; Nesoenas mayeri is the sister species to S. picturata, resulting in paraphyly of Streptopelia. Three main clades of Streptopelia are identified: (1) S. chinensis plus S. senegalensis, (2) S. picturata plus Nesoenas mayeri, and (3) all other species of Streptopelia. It is unclear whether those clades form a monophyletic group to the exclusion of Old World Columba, but several analyses produce that result. Species of Old World Columba are closely related to Streptopelia, with species of New World Columba clustering outside that group. Taxonomic changes suggested by our results include merging Nesoenas with Streptopelia and changing the generic name for New World Columba species to Patagioenas. Vocal similarities between S. picturata and N. mayeri are striking, given the general diversity of vocalizations in other species.

scholarly journals Progress, pitfalls and parallel universes: a history of insect phylogenetics

2016 ◽  
Vol 13 (121) ◽  
pp. 20160363 ◽  
Author(s):  
Karl M. Kjer ◽  
Chris Simon ◽  
Margarita Yavorskaya ◽  
Rolf G. Beutel
Keyword(s):  
Morphological Evolution ◽  
Large Datasets ◽  
Phylogenetic Studies ◽  
Number Of Genes ◽  
Molecular Phylogenetic ◽  
Parallel Universes ◽  
Methodological Improvement ◽  
History Of ◽  
New Challenges

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985–2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

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