scholarly journals Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants

2017 ◽  
Vol 91 (21) ◽  
Author(s):  
Zigui Chen ◽  
Wendy C. S. Ho ◽  
Siaw Shi Boon ◽  
Priscilla T. Y. Law ◽  
Martin C. W. Chan ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Gene Flow ◽  
East Asia ◽  
Evolutionary History ◽  
Homo Sapiens ◽  
Human Papillomaviruses ◽  
Oncogenic Potential ◽  
Content Type ◽  
History Of ◽  
Highest Posterior Density

ABSTRACT Human papillomavirus 58 (HPV58) is found in 10 to 18% of cervical cancers in East Asia but is rather uncommon elsewhere. The distribution and oncogenic potential of HPV58 variants appear to be heterogeneous, since the E7 T20I/G63S variant is more prevalent in East Asia and confers a 7- to 9-fold-higher risk of cervical precancer and cancer. However, the underlying genomic mechanisms that explain the geographic and carcinogenic diversity of HPV58 variants are still poorly understood. In this study, we used a combination of phylogenetic analyses and bioinformatics to investigate the deep evolutionary history of HPV58 complete genome variants. The initial splitting of HPV58 variants was estimated to occur 478,600 years ago (95% highest posterior density [HPD], 391,000 to 569,600 years ago). This divergence time is well within the era of speciation between Homo sapiens and Neanderthals/Denisovans and around three times longer than the modern Homo sapiens divergence times. The expansion of present-day variants in Eurasia could be the consequence of viral transmission from Neanderthals/Denisovans to non-African modern human populations through gene flow. A whole-genome sequence signature analysis identified 3 amino acid changes, 16 synonymous nucleotide changes, and a 12-bp insertion strongly associated with the E7 T20I/G63S variant that represents the A3 sublineage and carries higher carcinogenetic potential. Compared with the capsid proteins, the oncogenes E7 and E6 had increased substitution rates indicative of higher selection pressure. These data provide a comprehensive evolutionary history and genomic basis of HPV58 variants to assist further investigation of carcinogenic association and the development of diagnostic and therapeutic strategies. IMPORTANCE Papillomaviruses (PVs) are an ancient and heterogeneous group of double-stranded DNA viruses that preferentially infect the cutaneous and mucocutaneous epithelia of vertebrates. Persistent infection by specific oncogenic human papillomaviruses (HPVs), including HPV58, has been established as the primary cause of cervical cancer. In this work, we reveal the complex evolutionary history of HPV58 variants that explains the heterogeneity of oncogenic potential and geographic distribution. Our data suggest that HPV58 variants may have coevolved with archaic hominins and dispersed across the planet through host interbreeding and gene flow. Certain genes and codons of HPV58 variants representing higher carcinogenic potential and/or that are under positive selection may have important implications for viral host specificity, pathogenesis, and disease prevention.

scholarly journals Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Laura M. Carroll ◽  
Martin Wiedmann
Keyword(s):  
Bacillus Cereus ◽  
Foodborne Pathogens ◽  
Evolutionary History ◽  
Reference Genome ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Content Type ◽  
Group Iii ◽  
History Of ◽  
Highest Posterior Density

ABSTRACT Cereulide-producing members of Bacillus cereus sensu lato group III (also known as emetic B. cereus) possess cereulide synthetase, a plasmid-encoded, nonribosomal peptide synthetase encoded by the ces gene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by emetic B. cereus has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize group III B. cereus sensu lato genomes which possess ces (ces positive) alongside their closely related, ces-negative counterparts (i) to assess the genomic diversity encompassed by emetic B. cereus and (ii) to identify potential ces loss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly available ces-positive group III B. cereus sensu lato genomes and the ces-negative genomes interspersed among them (n = 159), we show that emetic B. cereus is not clonal; rather, multiple lineages within group III harbor cereulide-producing strains, all of which share an ancestor incapable of producing cereulide (posterior probability = 0.86 to 0.89). Members of ST 26 share an ancestor that existed circa 1748 (95% highest posterior density [HPD] interval = 1246.89 to 1915.64) and first acquired the ability to produce cereulide before 1876 (95% HPD = 1641.43 to 1946.70). Within ST 26 alone, two subsequent ces gain events were observed, as well as three ces loss events, including among isolates responsible for B. cereus sensu lato toxicoinfection (i.e., “diarrheal” illness). IMPORTANCE B. cereus is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., emetic syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., diarrheal syndrome). Here, we show that emetic B. cereus is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some group III B. cereus sensu lato populations to oscillate between diarrheal and emetic foodborne pathogens over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereus sensu lato outbreaks, since some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.

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

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.

Hunter-gatherers on the best-seller list: Steven Pinker and the “Bellicose School's” treatment of forager violence

2014 ◽  
Vol 6 (4) ◽  
pp. 216-228 ◽  
Author(s):  
Richard B. Lee
Keyword(s):  
Homo Sapiens ◽  
Human Populations ◽  
Hunter Gatherers ◽  
Content Type ◽  
Lethal Violence ◽  
Use Of Data ◽  
Hunting And Gathering ◽  
History Of ◽  
Early Farmers ◽  
Philosophical Debates

Purpose – The question of violence in hunter-gatherer society has animated philosophical debates since at least the seventeenth century. Steven Pinker has sought to affirm that civilization, is superior to the state of humanity during its long history of hunting and gathering. The purpose of this paper is to draw upon a series of recent studies that assert a baseline of primordial violence by hunters and gatherers. In challenging this position the author draws on four decades of ethnographic and historical research on hunting and gathering peoples. Design/methodology/approach – At the empirical heart of this question is the evidence pro- and con- for high rates of violent death in pre-farming human populations. The author evaluates the ethnographic and historical evidence for warfare in recorded hunting and gathering societies, and the archaeological evidence for warfare in pre-history prior to the advent of agriculture. Findings – The view of Steven Pinker and others of high rates of lethal violence in hunters and gatherers is not sustained. In contrast to early farmers, their foraging precursors lived more lightly on the land and had other ways of resolving conflict. With little or no fixed property they could easily disperse to diffuse conflict. The evidence points to markedly lower levels of violence for foragers compared to post-Neolithic societies. Research limitations/implications – This conclusion raises serious caveats about the grand evolutionary theory asserted by Steven Pinker, Richard Wrangham and others. Instead of being “killer apes” in the Pleistocene and Holocene, the evidence indicates that early humans lived as relatively peaceful hunter-gathers for some 7,000 generations, from the emergence of Homo sapiens up until the invention of agriculture. Therefore there is a major gap between the purported violence of the chimp-like ancestors and the documented violence of post-Neolithic humanity. Originality/value – This is a critical analysis of published claims by authors who contend that ancient and recent hunter-gatherers typically committed high levels of violent acts. It reveals a number of serious flaws in their arguments and use of data.

Human Evolution

1984 ◽  
Vol 8 ◽  
pp. 182-198
Author(s):  
Catherine Badgley
Keyword(s):  
Human Evolution ◽  
Evolutionary History ◽  
Pan Paniscus ◽  
Homo Sapiens ◽  
Great Apes ◽  
Sister Group ◽  
The Family ◽  
History Of ◽  
Living Species ◽  
Single Living

The evolutionary history of humans is well understood in outline, compared to that of many other groups of mammals. But human evolution remains enigmatic in its details, and these are compelling both scientifically and personally because they relate to the biological uniqueness of humans. Humans are placed in the primate family Hominidae, which, in traditional classifications, contains a single living species, Homo sapiens. The closest living relatives of humans are great apes: the chimpanzees Pan paniscus and Pan troglodytes, the gorilla Gorilla gorilla, and the orangutan Pongo pygmaeus. These apes have traditionally been placed in the family Pongidae as the sister group of Hominidae. Living Hominidae and Pongidae, together with Hylobatidae (gibbons) comprise the modern representatives of the primate suborder Hominoidea.

scholarly journals The evolutionary history of bears is characterized by gene flow across species

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Vikas Kumar ◽  
Fritjof Lammers ◽  
Tobias Bidon ◽  
Markus Pfenninger ◽  
Lydia Kolter ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
History Of

scholarly journals Human Origin for Livestock-Associated Methicillin-Resistant Staphylococcus aureus

mBio ◽  
2012 ◽  
Vol 3 (2) ◽  
Author(s):  
J. Ross Fitzgerald
Keyword(s):  
Staphylococcus Aureus ◽  
Evolutionary History ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Agricultural Practices ◽  
Methicillin Resistant ◽  
Content Type ◽  
Zoonotic Infections ◽  
Ancestral Origin ◽  
Important Study ◽  
History Of

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of human morbidity and mortality worldwide. The emergence in the last decade of a livestock-associated MRSA (LA-MRSA) clone which also has the capacity to cause zoonotic infections in humans has raised important questions regarding its origin and its potential to cause human epidemics. An important study by L. B. Price et al. [mBio 3(1):e00305-11, 2012] provides evidence for a human ancestral origin for LA-MRSA, raising concerns about agricultural practices that may have contributed to its emergence and expansion. The study highlights the potential for comparative whole-genome sequencing of closely related strains to provide valuable insights into the evolutionary history of bacterial pathogens.

scholarly journals Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131

mSphere ◽  
2016 ◽  
Vol 1 (4) ◽  
Author(s):  
Timothy J. Johnson ◽  
Jessica L. Danzeisen ◽  
Bonnie Youmans ◽  
Kyle Case ◽  
Katharine Llop ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Single Molecule ◽  
Convergent Evolution ◽  
Evolutionary History ◽  
Gene Clusters ◽  
Content Type ◽  
E Coli ◽  
History Of ◽  
Evolutionary Success

ABSTRACT A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage’s success. The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with the H30R/C1 clade, whereas an F2:A1:B− plasmid is associated with the H30Rx/C2 clade. A series of plasmid gene losses, gains, and rearrangements involving IS26 likely led to the current plasmid complements within each ST131-H30 sublineage, which contain several overlapping gene clusters with putative functions in virulence and fitness, suggesting plasmid-mediated convergent evolution. Evidence suggests that the H30Rx/C2-associated F2:A1:B− plasmid type was present in strains ancestral to the acquisition of fluoroquinolone resistance and prior to the introduction of a multidrug resistance-encoding gene cassette harboring bla CTX-M-15. In vitro experiments indicated a host strain-independent low frequency of plasmid transfer, differential levels of plasmid stability even between closely related ST131-H30 strains, and possible epistasis for carriage of these plasmids within the H30R/Rx lineages. IMPORTANCE A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage’s success.

scholarly journals The past, present and future of ancient bacterial DNA

2020 ◽  
Vol 6 (7) ◽  
Author(s):  
Nicolas Arning ◽  
Daniel J. Wilson
Keyword(s):  
Demographic Transition ◽  
Dental Plaque ◽  
Evolutionary History ◽  
High Throughput Sequencing ◽  
Industrial Revolution ◽  
Environmental Isolates ◽  
Bacterial Dna ◽  
Content Type ◽  
The Past ◽  
History Of

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

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