A novel rubi-like virus in the Pacific electric ray (Tetronarce californica) reveals the complex evolutionary history of the Matonaviridae

AbstractRubella virus (RuV) is the causative agent of rubella (“German measles”) and remains a global health concern. Until recently, RuV was the only known member of the genus Rubivirus and the only virus species classified within the Matonaviridae family of positive-sense RNA viruses. Other matonaviruses, including two new rubella-like viruses, Rustrela virus and Ruhugu virus, have been identified in several mammalian species, along with more divergent viruses in fish and reptiles. To screen for the presence of additional novel rubella-like viruses we mined published transcriptome data using genome sequences from Rubella, Rustrela, and Ruhugu viruses as baits. From this, we identified a novel rubella-like virus in a transcriptome of Tetronarce californica (Pacific electric ray) that is more closely related to mammalian Rustrela virus than to the divergent fish matonavirus and indicative of a complex pattern of cross-species virus transmission. Analysis of host reads confirmed that the sample analysed was indeed from a Pacific electric ray, and two other viruses identified in this animal, from the Arenaviridae and Reoviridae, grouped with other fish viruses. These findings indicate that the evolutionary history of the Matonaviridae is more complex than previously thought and highlights the vast number of viruses still to be discovered.

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A Novel Rubi-Like Virus in the Pacific Electric Ray (Tetronarce californica) Reveals the Complex Evolutionary History of the Matonaviridae

Viruses ◽

10.3390/v13040585 ◽

2021 ◽

Vol 13 (4) ◽

pp. 585

Author(s):

Rebecca M. Grimwood ◽

Edward C. Holmes ◽

Jemma L. Geoghegan

Keyword(s):

Evolutionary History ◽

Mammalian Species ◽

Virus Transmission ◽

Health Concern ◽

Virus Species ◽

Vast Number ◽

The Pacific ◽

Positive Sense ◽

History Of ◽

Fish Viruses

Rubella virus (RuV) is the causative agent of rubella (“German measles”) and remains a global health concern. Until recently, RuV was the only known member of the genus Rubivirus and the only virus species classified within the Matonaviridae family of positive-sense RNA viruses. Recently, two new rubella-like matonaviruses, Rustrela virus and Ruhugu virus, have been identified in several mammalian species, along with more divergent viruses in fish and reptiles. To screen for the presence of additional novel rubella-like viruses, we mined published transcriptome data using genome sequences from Rubella, Rustrela, and Ruhugu viruses as baits. From this, we identified a novel rubella-like virus in a transcriptome of Tetronarce californica—order Torpediniformes (Pacific electric ray)—that is more closely related to mammalian Rustrela virus than to the divergent fish matonavirus and indicative of a complex pattern of cross-species virus transmission. Analysis of host reads confirmed that the sample analysed was indeed from a Pacific electric ray, and two other viruses identified in this animal, from the Arenaviridae and Reoviridae, grouped with other fish viruses. These findings indicate that the evolutionary history of the Matonaviridae is more complex than previously thought and highlights the vast number of viruses that remain undiscovered.

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Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates

Virus Evolution ◽

10.1093/ve/veaa064 ◽

2020 ◽

Vol 6 (2) ◽

Author(s):

Ashleigh F Porter ◽

John H -O Pettersson ◽

Wei-Shan Chang ◽

Erin Harvey ◽

Karrie Rose ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Animal Species ◽

Rna Viruses ◽

Mammalian Species ◽

Virus Transmission ◽

Whole Genome ◽

Ixodes Holocyclus ◽

Positive Sense ◽

Novel Variant ◽

History Of

Abstract The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera—Hepacivirus, Pegivirus, Pestivirus, and Flavivirus—each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.

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Pathogen emergence in changing ecosystems: RAD-seq reveals long evolutionary history of Phellinus noxius in east Asia, Australia, and the Pacific Islands

10.22541/au.162670289.98665561/v1 ◽

2021 ◽

Author(s):

Olga Kozhar ◽

Mee-Sook Kim ◽

Jorge Ibarra Caballero ◽

Ned Klopfenstein ◽

Phil Cannon ◽

...

Keyword(s):

East Asia ◽

Evolutionary History ◽

Pacific Islands ◽

Genetic Relationships ◽

Supervised Machine Learning ◽

Sequencing Data ◽

The Pacific ◽

Recent Emergence ◽

History Of ◽

Phellinus Noxius

Emerging pathogens have been increasing exponentially over the last century. The knowledge on whether these organisms are native to ecosystems or have been recently introduced is often of great importance. Understanding the ecological and evolutionary processes promoting emergence can help to control their spread and forecast epidemics. Using restriction site-associated DNA sequencing data, we studied genetic relationships, pathways of spread, and evolutionary history of Phellinus noxius, an emerging root-rotting fungus of unknown origin, in eastern Asia, Australia, and the Pacific Islands. We analyzed patterns of genetic variation using Bayesian inference, maximum likelihood phylogeny, populations splits and mixtures measuring correlations in allele frequencies and genetic drift, and finally applied coalescent based theory using approximate Bayesian computation (ABC) with supervised machine learning. Population structure analyses revealed five genetic groups with signatures of complex recent and ancient migration histories. The most probable scenario of ancient pathogen spread is movement from west to east: from Malaysia to the Pacific Islands, with subsequent spread to Taiwan and Australia. Furthermore, ABC analyses indicate that P. noxius spread occurred thousands of generations ago, contradicting previous assumptions that it was recently introduced in multiple areas. Our results suggest that recent emergence of P. noxius in east Asia, Australia, and the Pacific Islands is likely driven by anthropogenic and natural disturbances, including deforestation, land-use change, severe weather events, and introduction of exotic plants. This study provides a novel example of utilization of genome wide allele frequency data to unravel dynamics of pathogen emergence under conditions of changing ecosystems.

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INVESTIGATING THE EVOLUTIONARY HISTORY OF THE PACIFIC NORTHWEST MESIC FOREST ECOSYSTEM: HYPOTHESIS TESTING WITHIN A COMPARATIVE PHYLOGEOGRAPHIC FRAMEWORK

Evolution ◽

10.1111/j.0014-3820.2005.tb01815.x ◽

2005 ◽

Vol 59 (8) ◽

pp. 1639-1652 ◽

Cited By ~ 14

Author(s):

Brayan C. Cartens ◽

Steven J. Brunsfeld ◽

John R. Demboski ◽

Jeffrey M. Good ◽

Jack Sullivan

Keyword(s):

Hypothesis Testing ◽

Pacific Northwest ◽

Forest Ecosystem ◽

Evolutionary History ◽

Mesic Forest ◽

The Pacific ◽

History Of

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Long evolutionary history of an emerging fungal pathogen of diverse tree species in eastern Asia, Australia, and the Pacific Islands

10.22541/au.164079355.56023358/v1 ◽

2021 ◽

Author(s):

Olga Kozhar ◽

Mee-Sook Kim ◽

Jorge Ibarra Caballero ◽

Ned Klopfenstein ◽

Phil Cannon ◽

...

Keyword(s):

Evolutionary History ◽

Plant Pathogens ◽

Pacific Islands ◽

Genetic Relationships ◽

Supervised Machine Learning ◽

Sequencing Data ◽

Eastern Asia ◽

The Pacific ◽

Recent Emergence ◽

History Of

Emerging plant pathogens have been increasing exponentially over the last century. To address this issue, it is critical to determine whether these pathogens are native to ecosystems or have been recently introduced. Understanding the ecological and evolutionary processes fostering emergence can help to manage their spread and predict epidemics/epiphytotics. Using restriction site-associated DNA sequencing data, we studied genetic relationships, pathways of spread, and evolutionary history of Phellinus noxius, an emerging root-rotting fungus of unknown origin, in eastern Asia, Australia, and the Pacific Islands. We analyzed patterns of genetic variation using Bayesian inference, maximum likelihood phylogeny, populations splits and mixtures measuring correlations in allele frequencies and genetic drift, and finally applied coalescent based theory using Approximate Bayesian computation (ABC) with supervised machine learning. Population structure analyses revealed five genetic groups with signatures of complex recent and ancient migration histories. The most probable scenario of ancient pathogen spread is movement from ghost population to Malaysia and the Pacific Islands, with subsequent spread to Taiwan and Australia. Furthermore, ABC analyses indicate that P. noxius spread occurred thousands of generations ago, contradicting previous assumptions that this pathogen was recently introduced to multiple geographic regions. Our results suggest that recent emergence of P. noxius in eastern Asia, Australia, and the Pacific Islands is likely driven by anthropogenic and natural disturbances, such as deforestation, land-use change, severe weather events, and/or introduction of exotic plants. This study provides a novel example of applying genome-wide allele frequency data to unravel dynamics of pathogen emergence under changing ecosystem conditions.

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Expanding the RNA Virosphere by Unbiased Metagenomics

Annual Review of Virology ◽

10.1146/annurev-virology-092818-015851 ◽

2019 ◽

Vol 6 (1) ◽

pp. 119-139 ◽

Cited By ~ 26

Author(s):

Yong-Zhen Zhang ◽

Yan-Mei Chen ◽

Wen Wang ◽

Xin-Chen Qin ◽

Edward C. Holmes

Keyword(s):

Evolutionary History ◽

Genetic Material ◽

Virus Species ◽

Future Directions ◽

Important Species ◽

Virus Diversity ◽

Limited Perspective ◽

Etiologic Agents ◽

History Of ◽

Overt Disease

Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field.

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Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae

Journal of General Virology ◽

10.1099/vir.0.047928-0 ◽

2013 ◽

Vol 94 (4) ◽

pp. 738-748 ◽

Cited By ~ 45

Author(s):

Ying Tao ◽

Mang Shi ◽

Christina Conrardy ◽

Ivan V. Kuzmin ◽

Sergio Recuenco ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Evolutionary History ◽

Evolutionary Rate ◽

Mammalian Species ◽

Evolutionary Analysis ◽

Viral Pathogens ◽

Genomic Features ◽

Wide Range ◽

History Of ◽

Multiple Species

Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic diversity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus–host co-divergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.

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Eggs of echinoids separated by the Isthmus of Panama harbor divergent microbiota

Marine Ecology Progress Series ◽

10.3354/meps13424 ◽

2020 ◽

Vol 648 ◽

pp. 169-177

Author(s):

TJ Carrier ◽

HA Lessios ◽

AM Reitzel

Keyword(s):

Community Composition ◽

Bacterial Communities ◽

Evolutionary History ◽

Isthmus Of Panama ◽

The Pacific ◽

Species Pairs ◽

History Of ◽

The Pacific Ocean ◽

The Caribbean ◽

Bodies Of Water

Relationships between animals and their associated microbiota are dependent on both the evolutionary history of the host and on the environment. The majority of studies tend to focus on either one of these factors but rarely consider how both determine the community composition of the associated microbiota. One ‘natural experiment’ to test how evolutionary history, shared environments, and the interaction between these factors drive community composition is to compare geminate species pairs. Echinoids separated by the Isthmus of Panama are suitable for this comparison due to their known evolutionary history and differences in the oceanographic characteristics of the Caribbean Sea and the Pacific Ocean. By comparing the bacterial communities of the eggs of Echinometra and Diadema geminate species pairs, we show that each pair of geminate species associates with a distinct bacterial community in a pattern consistent with phylosymbiosis, and that the interaction between the evolutionary history of the host and the environment best explains differences in these communities. Moreover, we found that the relative abundance of particular bacterial taxa differed considerably between the 2 bodies of water and that the 2 Caribbean Echinometra species were dominated by unclassified bacterial taxa within the phototrophic Oxyphotobacteria. Taken together, data presented here support the hypothesis that the bacterial communities associated with geminate species are another characteristic of these species that have diverged in ~2.8 million years of isolation.

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A new species of Cythere (Ostracoda) from the Middle Eocene McIntosh Formation, Doty Hills, Washington State, USA, and its significance for the evolutionary history of the genus

Journal of Paleontology ◽

10.1017/s0022336000058418 ◽

2010 ◽

Vol 84 (4) ◽

pp. 709-719

Author(s):

Tatsuhiko Yamaguchi ◽

James L. Goedert

Keyword(s):

Evolutionary History ◽

Middle Eocene ◽

Washington State ◽

Northwestern Pacific ◽

The Pacific ◽

Northeastern Pacific ◽

History Of ◽

The Pacific Ocean ◽

Western Washington ◽

A New Species

Cythere ikeyanoriyukii n. sp., an extant phytal ostracode genus, was obtained from the Middle Eocene McIntosh Formation in the Doty Hills, western Washington State, USA. It was associated with eleven taxa, which are extant phytal and shelfal genera such as Loxocorniculum, Xestoleberis, Ambostracon, Coquimba, and Acanthocythereis. The presence of Cythere in this assemblage is surprising and indicates that the first appearance of this genus was middle Eocene time at the latest, or at least 20 Ma earlier than previously thought. Cythere did not originate in the Pacific Ocean around Japan as previously thought, but instead must have migrated from the northeastern Pacific to the northwestern Pacific between middle Eocene and early Miocene time.

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