scholarly journals 100-My history of bornavirus infections hidden in vertebrate genomes

2021 ◽  
Vol 118 (20) ◽  
pp. e2026235118
Author(s):  
Junna Kawasaki ◽  
Shohei Kojima ◽  
Yahiro Mukai ◽  
Keizo Tomonaga ◽  
Masayuki Horie
Keyword(s):  
Phylogenetic Analyses ◽  
Migration Route ◽  
Messenger Rnas ◽  
Molecular Fossil ◽  
History Of ◽  
Geographic Distributions ◽  
Fossil Records ◽  
Insight Into ◽  
Animal Genomes

Although viruses have threatened our ancestors for millions of years, prehistoric epidemics of viruses are largely unknown. Endogenous bornavirus-like elements (EBLs) are ancient bornavirus sequences derived from the viral messenger RNAs that were reverse transcribed and inserted into animal genomes, most likely by retrotransposons. These elements can be used as molecular fossil records to trace past bornaviral infections. In this study, we systematically identified EBLs in vertebrate genomes and revealed the history of bornavirus infections over nearly 100 My. We confirmed that ancient bornaviral infections have occurred in diverse vertebrate lineages, especially in primate ancestors. Phylogenetic analyses indicated that primate ancestors were infected with various bornaviral lineages during evolution. EBLs in primate genomes formed clades according to their integration ages, suggesting that bornavirus lineages infected with primate ancestors had changed chronologically. However, some bornaviral lineages may have coexisted with primate ancestors and underwent repeated endogenizations for tens of millions of years. Moreover, a bornaviral lineage that coexisted with primate ancestors also endogenized in the genomes of some ancestral bats. The habitats of these bat ancestors have been reported to overlap with the migration route of primate ancestors. These results suggest that long-term virus–host coexistence expanded the geographic distributions of the bornaviral lineage along with primate migration and may have spread their infections to these bat ancestors. Our findings provide insight into the history of bornavirus infections over geological timescales that cannot be deduced from research using extant viruses alone, thus broadening our perspective on virus–host coevolution.

scholarly journals One hundred million years history of bornavirus infections hidden in vertebrate genomes

2020 ◽  
Author(s):  
Junna Kawasaki ◽  
Shohei Kojima ◽  
Yahiro Mukai ◽  
Keizo Tomonaga ◽  
Masayuki Horie
Keyword(s):  
Viral Infections ◽  
Phylogenetic Analyses ◽  
Migration Route ◽  
Chronological Change ◽  
History Of ◽  
New Hosts ◽  
Geographic Distributions ◽  
Fossil Records ◽  
Viral Lineage

AbstractAlthough viruses have threatened our ancestors for millions of years, prehistoric epidemics of viruses are largely unknown. Endogenous bornavirus-like elements (EBLs) are ancient viral sequences that have been integrated into animal genomes. These elements can be used as molecular fossil records to trace past bornaviral infections. In this study, we systematically identified EBLs in vertebrate genomes and revealed the history of bornavirus infections over nearly 100 million years. We found that ancient bornaviral infections have occurred in diverse vertebrate lineages, especially in primate ancestors. Phylogenetic analyses indicated that primate ancestors had been infected with various bornaviral lineages during evolution. Moreover, EBLs in primate genomes formed clades according to their integration ages, suggesting that epidemic lineages of bornaviruses had changed chronologically. However, we found that some bornaviral lineages coexisted with primate ancestors and underwent repeated endogenizations for tens of millions of years. Furthermore, this viral lineage that coexisted with primate ancestors was also endogenized in some ancestral bats. Notably, the geographic distributions of these bat ancestors have been reported to overlap with the migration route of primate ancestors, suggesting that long-term virus-host coexistence could have expanded the geographic distributions of the viral lineage and might have spread their infections to new hosts. Thus, our findings describe hidden virus-host co-evolutionary history over geological timescales, including chronological change in epidemic bornaviral lineages, long-term virus-host coexistence, and expansion of viral infections.

scholarly journals Phylogenetic studies of eucalypts: fossils, morphology and genomes

2016 ◽  
Vol 128 (1) ◽  
pp. 12 ◽  
Author(s):  
Michael J. Bayly
Keyword(s):  
Dna Sequencing ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Phylogenetic Studies ◽  
Recent Advances ◽  
History Of ◽  
Morphological And Molecular Data ◽  
Economic Use ◽  
Insight Into

The eucalypt group includes seven genera: Eucalyptus, Corymbia, Angophora, Eucalyptopsis, Stockwellia, Allosyncarpia and Arillastrum. Knowledge of eucalypt phylogeny underpins classification of the group, and facilitates understanding of their ecology, conservation and economic use, as well as providing insight into the history of Australia’s flora. Studies of fossils and phylogenetic analyses of morphological and molecular data have made substantial contributions to understanding of eucalypt relationships and biogeography, but relationships among some genera are still uncertain, and there is controversy about generic circumscription of the bloodwood eucalypts (genus Corymbia). Relationships at lower taxonomic levels, e.g. among sections and series of Eucalyptus, are also not well resolved. Recent advances in DNA sequencing methods offer the ability to obtain large genomic datasets that will enable improved understanding of eucalypt evolution.

scholarly journals Postglacial Fire Frequency and its Relation to Long-Term Vegetational and Climatic Changes in Yellowstone Park

1992 ◽  
Vol 16 ◽  
pp. 212-218
Author(s):  
Cathy Whitlock
Keyword(s):  
Fire Regime ◽  
Fire Frequency ◽  
Northern Rocky Mountains ◽  
Modern Pollen ◽  
Pollen Rain ◽  
History Of ◽  
Fossil Records ◽  
In Fire ◽  
The Relationship

The primary research objective has been to study the vegetational history of Yellowstone and its sensitivity to changes in climate and fire frequency. To establish a sequence of vegetational changes, a network of pollen records spanning the last 14,000 years has been studied from different types of vegetation within the Park. The relationship between modern pollen rain, modern vegetation and present­day climate in the northern Rocky Mountains has been the basis for interpreting past vegetation and climate from the fossil records. Changes in fire regime during the past 14,000 years have been inferred from sedimentary charcoal and other fire proxy in lake sediments. Calibration of the fire signal is based on a study that measures the input of charcoal into lakes following the 1988 fires in Yellowstone.

scholarly journals Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
E. Hekkala ◽  
J. Gatesy ◽  
A. Narechania ◽  
R. Meredith ◽  
M. Russello ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Sister Group Relationship ◽  
Molecular Fossil ◽  
Close Relationship ◽  
History Of ◽  
Competing Hypotheses

AbstractAncient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of the extinct “horned” crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

scholarly journals The Discerning Ear: Cardiac Auscultation in the Era of Artificial Intelligence and Telemedicine

2021 ◽  
Author(s):  
Vivek Jani ◽  
David A Danford ◽  
W Reid Thompson ◽  
Andreas Schuster ◽  
Cedric Manlhiot ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Computer Assisted ◽  
Cardiac Auscultation ◽  
Cardiac Murmur ◽  
New Era ◽  
History Of ◽  
The Impact ◽  
Paradigm Shifting ◽  
Insight Into

Abstract Heart murmur, a thoracic auscultatory finding of cardiovascular origin, is extremely common in childhood and can appear at any age from premature newborn to late adolescence. The objective of this review is to provide a modern examination and update of cardiac murmur auscultation in this new era of artificial intelligence and telemedicine. First, we provide a comprehensive review of the causes and differential diagnosis, clinical features, evaluation, and long-term management of pediatric heart murmurs. Next, we provide a brief history of computer-assisted auscultation and murmur analysis, along with insight into the engineering design of the digital stethoscope. We conclude with a discussion of the paradigm shifting impact of deep learning on murmur analysis, artificial intelligence assisted auscultation, and the implications of these technologies on telemedicine in pediatric cardiology. It is our hope that this article provides an updated perspective on the impact of artificial intelligence on cardiac auscultation for the modern pediatric cardiologist.

scholarly journals Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

2020 ◽  
Author(s):  
Spyros Lytras ◽  
Gloria Arriagada ◽  
Robert J. Gifford
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Dna Viruses ◽  
History Of ◽  
Selective Forces ◽  
Cenozoic Era ◽  
Vertebrate Hosts ◽  
New Perspective ◽  
Animal Genomes

ABSTRACTHepadnaviruses (family Hepadnaviviridae) are reverse-transcribing animal viruses that infect vertebrates. Vertebrate genomes contain DNA sequences derived from ancient hepadnaviruses, and these ‘endogenous hepatitis B viruses’ (eHBVs) reveal aspects of the long-term coevolutionary relationship between hepadnaviruses and their vertebrate hosts. Here, we use a novel, data-oriented approach to recover and analyse the complete repertoire of eHBV elements in published animal genomes. We show that germline incorporation of hepadnaviruses is exclusive to a single vertebrate group (Sauria) and that the eHBVs contained in saurian genomes represent a far greater diversity of hepadnaviruses than previously recognised. Through in-depth characterisation of eHBV elements we establish the existence of four distinct subgroups within the genus Avihepadnavirus and trace their evolution through the Cenozoic Era. Furthermore, we provide a completely new perspective on hepadnavirus evolution by showing that the metahepadnaviruses (genus Metahepadnavirus) originated >300 million years ago in the Paleozoic Era, and has historically infected a broad range of vertebrates. We also show that eHBVs have been intra-genomically amplified in some saurian lineages, and that eHBVs located at approximately equivalent genomic loci have been acquired in entirely distinct germline integration events. These findings indicate that selective forces have favoured the accumulation of hepadnaviral sequences at specific loci in the saurian germline. Our investigation provides a range of new insights into the long-term evolutionary history of reverse-transcribing DNA viruses and demonstrates that germline incorporation of hepadnaviruses has played an important role in shaping the evolution of saurian genomes.

Koolen-de Vries Syndrome: Clinical Report of an Adult and Literature Review

2016 ◽  
Vol 150 (1) ◽  
pp. 40-45 ◽  
Author(s):  
Claudia Ciaccio ◽  
Chiara Dordoni ◽  
Marco Ritelli ◽  
Marina Colombi
Keyword(s):  
Joint Hypermobility ◽  
Clinical Report ◽  
Ehlers Danlos Syndrome ◽  
Variable Level ◽  
Fourth Decade ◽  
De Vries ◽  
History Of ◽  
Danlos Syndrome ◽  
Insight Into

Koolen-de Vries syndrome (KdS) is a rare genetic condition characterized by typical facial dysmorphisms, cardiac and renal defects, skeletal anomalies, developmental delay, and intellectual disability of variable level. It is caused by a 440-680-kb deletion in the 17q21.31 region, encompassing CRHR1, MAPT, IMP5, STH, and KANSL1, or by an intragenic KANSL1 mutation. The majority of the patients reported are pediatric or young adults, and long-term studies able to define the prognosis of the disease are lacking. Here, we report a patient in the fourth decade misdiagnosed in the past as classical Ehlers-Danlos syndrome for the presence of generalized joint hypermobility, who carried a 546-kb deletion in 17q21.31, and compare his phenotype with those of the few KdS adults (aged >18 years) described so far. We observed a favorable prognosis of epilepsy and cardiovascular signs and reduction of joint hypermobility with age, thus providing insight into the natural history of the disorder.

scholarly journals Buchnera has changed flatmate but the repeated replacement of co-obligate symbionts is not associated with the ecological expansions of their aphid hosts

2016 ◽  
Author(s):  
A.S. Meseguer ◽  
A. Manzano-Marín ◽  
A. Coeur d’Acier ◽  
A-L. Clamens ◽  
M. Godefroid ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Aphid Species ◽  
Buchnera Aphidicola ◽  
Evolutionary Transitions ◽  
Symbiotic Associations ◽  
Metabolic Functions ◽  
History Of ◽  
Serratia Symbiotica ◽  
Bacterial Genes

AbstractSymbiotic associations with bacteria have facilitated important evolutionary transitions in insects and resulted in long-term obligate interactions. Recent evidence suggests that these associations are not always evolutionarily stable and that symbiont replacement and/or supplementation of an obligate symbiosis by an additional bacterium has occurred during the history of many insect groups. Yet, the factors favoring one symbiont over another in this evolutionary dynamic are not well understood; progress has been hindered by our incomplete understanding of the distribution of symbionts across phylogenetic and ecological contexts. While many aphids are engaged into an obligate symbiosis with a single Gammaproteobacterium, Buchnera aphidicola, in species of the Lachninae subfamily, this relationship has evolved into a “ménage à trois”, in which Buchnera is complemented by a cosymbiont, usually Serratia symbiotica. Using deep sequencing of 16S rRNA bacterial genes from 128 species of Cinara (the most diverse Lachninae genus), we reveal a highly dynamic dual symbiotic system in this aphid lineage. Most species host both Serratia and Buchnera but, in several clades, endosymbionts related to Sodalis, Erwinia or an unnamed member of the Enterobacteriaceae have replaced Serratia. Endosymbiont genome sequences from four aphid species+confirm that these coresident symbionts fulfill essential metabolic functions not ensured by Buchnera. We further demonstrate through comparative phylogenetic analyses that co-symbiont replacement is not associated with the adaptation of aphids to new ecological conditions. We propose that symbiont succession was driven by factors intrinsic to the phenomenon of endosymbiosis, such as rapid genome deterioration or competitive interactions between bacteria with similar metabolic capabilities.

scholarly journals A new species of Eogruidae (Aves: Gruiformes) from the Miocene of the Linxia Basin, Gansu, China: Evolutionary and climatic implications

The Auk ◽  
2019 ◽  
Vol 137 (1) ◽  
Author(s):  
Grace Musser ◽  
Zhiheng Li ◽  
Julia A Clarke
Keyword(s):  
New Species ◽  
Northwest China ◽  
Biogeographic History ◽  
Linxia Basin ◽  
History Of ◽  
Key Drivers ◽  
Fossil Records ◽  
Present Description ◽  
A New Species ◽  
Insight Into

Abstract Despite having one of the most robust fossil records within core-gruiform birds (rails, cranes, and allies), the biogeographic history of Gruidae (cranes) and key drivers of diversification within this group remain largely unknown. The Eogruidae of Eurasia represent some of the earliest known crane-like fossils. Here, we present description of a new species represented by a well-preserved specimen of a foot from the late Miocene (7–6.5 mya) Liushu Formation of Linxia Basin, Gansu, China. It is the only eogruid fossil that has been found in this formation and is the first eogruid known from northwest China. Linxia Basin is located along the margin of the northeastern Tibetan Plateau, which allows for new insight into Miocene dispersal of the Eogruidae and potential climatological and geological connections. It is also the first specimen with an associated tarsometatarsus and nearly complete phalanges, including a claw, which provides further morphological information on this taxon. Referral of the new specimen to Eogruidae is based on extreme reduction of the trochlea of metatarsal II, which is most similar to the condition present in the eogruid subclade traditionally termed Ergilornithidae.

scholarly journals Comparison among the first representative chloroplast genomes of Orontium, Lasia, Zamioculcas, and Stylochaeton of the plant family Araceae: inverted repeat dynamics are not linked to phylogenetic signaling

2020 ◽  
Author(s):  
Abdullah ◽  
Claudia L. Henriquez ◽  
Furrukh Mehmood ◽  
Iram Shahzadi ◽  
Zain Ali ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
History Of ◽  
Contraction And Expansion ◽  
Insight Into

AbstractThe chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of the first representatives of four genera representing three subfamilies: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using the plastomes. The size of the chloroplast genomes ranged from 163,770–169,982 bp. These genomes comprise 114 unique genes, including 80 protein-coding, 4 rRNA, and 30 tRNA genes. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The junctions JSB (IRb/SSC) and JSA (SSC/IRa) are highly variable, as is oligonucleotide repeats content among the genomes. The patterns of inverted repeats contraction and expansion were shown to be homoplasious and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were shown for several genes in S. bogneri. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

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