scholarly journals Phylogeographic analysis of Pseudogymnoascus destructans partitivirus-pa explains the spread dynamics of white-nose syndrome in North America

2021 ◽  
Vol 17 (3) ◽  
pp. e1009236
Author(s):  
Vaskar Thapa ◽  
Gregory G. Turner ◽  
Marilyn J. Roossinck
Keyword(s):  
North America ◽  
Geographic Origin ◽  
Recent Common Ancestor ◽  
Analysis Tool ◽  
Pseudogymnoascus Destructans ◽  
Long Distance ◽  
Phylogeographic Analysis ◽  
White Nose Syndrome ◽  
Most Recent Common Ancestor ◽  
Beast Analysis

Understanding the dynamics of white-nose syndrome spread in time and space is an important component for the disease epidemiology and control. We reported earlier that a novel partitivirus, Pseudogymnoascus destructans partitivirus-pa, had infected the North American isolates of Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome in bats. We showed that the diversity of the viral coat protein sequences is correlated to their geographical origin. Here we hypothesize that the geographical adaptation of the virus could be used as a proxy to characterize the spread of white-nose syndrome. We used over 100 virus isolates from diverse locations in North America and applied the phylogeographic analysis tool BEAST to characterize the spread of the disease. The strict clock phylogeographic analysis under the coalescent model in BEAST showed a patchy spread pattern of white-nose syndrome driven from a few source locations including Connecticut, New York, West Virginia, and Kentucky. The source states had significant support in the maximum clade credibility tree and Bayesian stochastic search variable selection analysis. Although the geographic origin of the virus is not definite, it is likely the virus infected the fungus prior to the spread of white-nose syndrome in North America. We also inferred from the BEAST analysis that the recent long-distance spread of the fungus to Washington had its root in Kentucky, likely from the Mammoth cave area and most probably mediated by a human. The time to the most recent common ancestor of the virus is estimated somewhere between the late 1990s to early 2000s. We found the mean substitution rate of 2 X 10−3 substitutions per site per year for the virus which is higher than expected given the persistent lifestyle of the virus, and the stamping-machine mode of replication. Our approach of using the virus as a proxy to understand the spread of white-nose syndrome could be an important tool for the study and management of other infectious diseases.

scholarly journals Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Kevin P. Drees ◽  
Jeffrey M. Lorch ◽  
Sebastien J. Puechmaille ◽  
Katy L. Parise ◽  
Gudrun Wibbelt ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
North American ◽  
Fungal Pathogen ◽  
Phylogenetic Study ◽  
Pseudogymnoascus Destructans ◽  
Long Distance ◽  
Recent Introduction ◽  
White Nose Syndrome ◽  
The North

ABSTRACT Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans , a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans . Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia. IMPORTANCE This phylogenetic study of the bat white-nose syndrome agent, P. destructans , uses genomics to elucidate evolutionary relationships among populations of the fungal pathogen to understand the epizoology of this biological invasion. We analyze hypervariable and abundant genetic characters (microsatellites and genomic SNPs, respectively) to reveal previously uncharacterized diversity among populations of the pathogen from North America and Eurasia. We present new evidence supporting recent introduction of the fungus to North America from a diverse Eurasian population, with limited increase in genetic variation in North America since that introduction.

scholarly journals Target Capture Sequencing Unravels Rubus Evolution

2019 ◽  
Author(s):  
Katherine A. Carter ◽  
Aaron Liston ◽  
Nahla V. Bassil ◽  
Lawrence A. Alice ◽  
Jill M. Bushakra ◽  
...  
Keyword(s):  
North America ◽  
Dna Sequences ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Long Distance ◽  
Ploidy Levels ◽  
Most Recent Common Ancestor ◽  
Target Capture ◽  
Target Capture Sequencing ◽  
Capture Sequencing

AbstractBackgroundRubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to: estimate the phylogeny of 94 geographically diverse species and 3 cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification.ResultsTarget capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene.ConclusionsRubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. Target capture sequencing confirmed that most subgenera are para- or polyphyletic. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus taxonomic and phylogenetic research.

Prevalence and phenology of white-nose syndrome fungus Pseudogymnoascus destructans in bats from Poland

2014 ◽  
Vol 9 (4) ◽  
pp. 437-443 ◽  
Author(s):  
Konrad Sachanowicz ◽  
Arkadiusz Stępień ◽  
Mateusz Ciechanowski
Keyword(s):  
North America ◽  
Mass Mortality ◽  
Parasitic Fungus ◽  
Pseudogymnoascus Destructans ◽  
Southern Poland ◽  
White Nose Syndrome ◽  
Two Samples ◽  
Myotis Myotis ◽  
Myotis Daubentonii ◽  
Fungal Dna

AbstractPseudogymnoascus destructans (Pd), a parasitic fungus (being responsible for a disease known as white-nose syndrome, WNS) that caused mass mortality of cave-dwelling, hibernating bats in North America, appears to be native of Europe, where it also occurs on wintering bats, but no similar outbreaks of WNS have been recorded. Herein, we provide the first account on prevalence and phenology of P. destructans in Poland. Bats were counted once per month, from October or January to May (2010-2013), in an abandoned ore mine in southern Poland. Presence of P. destructans in two samples was confirmed by sequencing of isolated fungal DNA. Observations of phenotypically identical mycosis on bats hibernating at this site in March 2006 are likely to be the first known records of P. destructans from Poland. All Pd-suspected individuals were Myotis myotis with an exception of one Myotis daubentonii. The first Pd-suspected bats were noted in mid-February, but their number was the highest in March, what overlapped with maximum numbers of hibernating M. myotis. The prevalence in March was 7%–27% of M. myotis individuals. No mass mortality of bats was observed in the mine, with only three dead individuals found in the hibernaculum which hosted up to 130 bats, representing 6–7 species.

scholarly journals Complete Genome Analysis of 33 Ecologically and Biologically Diverse Rift Valley Fever Virus Strains Reveals Widespread Virus Movement and Low Genetic Diversity due to Recent Common Ancestry

2006 ◽  
Vol 81 (6) ◽  
pp. 2805-2816 ◽  
Author(s):  
Brian H. Bird ◽  
Marina L. Khristova ◽  
Pierre E. Rollin ◽  
Thomas G. Ksiazek ◽  
Stuart T. Nichol
Keyword(s):  
Genetic Diversity ◽  
Rift Valley ◽  
Complete Genome ◽  
Rift Valley Fever ◽  
Geographic Origin ◽  
Recent Common Ancestor ◽  
Virus Movement ◽  
Long Distance ◽  
Valley Fever ◽  
Virus Strains

ABSTRACT Rift Valley fever (RVF) virus is a mosquito-borne RNA virus responsible for large explosive outbreaks of acute febrile disease in humans and livestock in Africa with significant mortality and economic impact. The successful high-throughput generation of the complete genome sequence was achieved for 33 diverse RVF virus strains collected from throughout Africa and Saudi Arabia from 1944 to 2000, including strains differing in pathogenicity in disease models. While several distinct virus genetic lineages were determined, which approximately correlate with geographic origin, multiple exceptions indicative of long-distance virus movement have been found. Virus strains isolated within an epidemic (e.g., Mauritania, 1987, or Egypt, 1977 to 1978) exhibit little diversity, while those in enzootic settings (e.g., 1970s Zimbabwe) can be highly diverse. In addition, the large Saudi Arabian RVF outbreak in 2000 appears to have involved virus introduction from East Africa, based on the close ancestral relationship of a 1998 East African virus. Virus genetic diversity was low (∼5%) and primarily involved accumulation of mutations at an average of 2.9 × 10−4 substitutions/site/year, although some evidence of RNA segment reassortment was found. Bayesian analysis of current RVF virus genetic diversity places the most recent common ancestor of these viruses in the late 1800s, the colonial period in Africa, a time of dramatic changes in agricultural practices and introduction of nonindigenous livestock breeds. In addition to insights into the evolution and ecology of RVF virus, these genomic data also provide a foundation for the design of molecular detection assays and prototype vaccines useful in combating this important disease.

Huehuecanauhtlus tiquichensis, a new hadrosauroid dinosaur (Ornithischia: Ornithopoda) from the Santonian (Late Cretaceous) of Michoacán, Mexico

2012 ◽  
Vol 49 (2) ◽  
pp. 379-395 ◽  
Author(s):  
Angel Alejandro Ramírez-Velasco ◽  
Mouloud Benammi ◽  
Albert Prieto-Márquez ◽  
Jesús Alvarado Ortega ◽  
René Hernández-Rivera
Keyword(s):  
North America ◽  
Late Cretaceous ◽  
Common Ancestor ◽  
Cladistic Analysis ◽  
Lateral View ◽  
Occlusal Plane ◽  
Recent Common Ancestor ◽  
Vicariant Event ◽  
Most Recent Common Ancestor ◽  
Caudal Vertebrae

Huehuecanauhtlus tiquichensis gen. et sp. nov. is the southernmost diagnostic basal hadrosauroid in the Americas. The holotype and referred material of this taxon came from Santonian strata in the Michoacán State, southwestern Mexico. Huehuecanauhtlus tiquichensis is diagnosed on the basis of a combination of dental, axial, and appendicular characters, including the following: at least two teeth exposed on the occlusal plane of the dentary and maxilla; seven sacral vertebrae; tall neural spines of caudal vertebrae; supraacetabular process long; and short and trapezoidal (in lateral view) postacetabular process. It differs from other hadrosauroids in having an ilium with extreme ventral deflection of the preacetabular process. Maximum parsimony cladistic analysis placed H. tiquichensis as a closely related outgroup to Hadrosauridae. The occurrence of H. tiquichensis in the Santonian of North America may be explained as a dispersal event from Asia to North America that occurred no later than the Albian or, alternatively, as a vicariant event of a most recent common ancestor widespread in both landmasses.

scholarly journals Ten-year projection of white-nose syndrome disease dynamics at the southern leading-edge of infection in North America

2020 ◽  
Author(s):  
Melissa B. Meierhofer ◽  
Thomas M. Lilley ◽  
Lasse Ruokolainen ◽  
Joseph S. Johnson ◽  
Steven Parratt ◽  
...  
Keyword(s):  
Infectious Disease ◽  
North America ◽  
Environmental Conditions ◽  
Leading Edge ◽  
Environmental Data ◽  
Disease Spread ◽  
Disease Dynamics ◽  
Pseudogymnoascus Destructans ◽  
White Nose Syndrome ◽  
Management Actions

AbstractPredicting the emergence and spread of infectious diseases is critical for effective conservation of biodiversity. White-nose syndrome (WNS), an emerging infectious disease of bats, has resulted in high mortality in eastern North America. Because the fungal causative agent Pseudogymnoascus destructans is constrained by temperature and humidity, spread dynamics may vary greatly by geography. Environmental conditions in the southern part of the continent, where disease dynamics are typically studied, making it difficult to predict how the disease will manifest. Herein, we modeled the spread of WNS in Texas based on available cave densities and average dispersal distances of species occupying these sites, and projected these results out to 10 years. We parameterized a predictive model of WNS epidemiology and its effects on hibernatory bat populations with observed environmental data from bat hibernation sites in Texas. Our model suggests that bat populations in northern Texas will be more affected by WNS mortality than southern Texas. As such, we recommend prioritizing the preservation of large overwintering colonies of bats in north Texas through management actions. Our model further illustrates that infectious disease spread and infectious disease severity can become uncoupled over a gradient of environmental variation. Finally, our results highlight the importance of understanding host, pathogen and environmental conditions in various settings to elucidate what may happen across a breadth of environments.

scholarly journals Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic

2015 ◽  
Vol 90 (3) ◽  
pp. 1244-1258 ◽  
Author(s):  
Natalie N. Kinloch ◽  
Daniel R. MacMillan ◽  
Anh Q. Le ◽  
Laura A. Cotton ◽  
David R. Bangsberg ◽  
...  
Keyword(s):  
North America ◽  
North American ◽  
Consensus Sequence ◽  
Hla Class I ◽  
Class I ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Subtype B ◽  
Hiv 1 ◽  
Over Time

ABSTRACTHuman leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989;n= 338) and modern (2001 to 2011;n= 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era.IMPORTANCEHLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may accumulate in circulation over time, potentially undermining host antiviral immunity to the transmitted viral strain. We studied >600 experimentally collected HIV-1 polymerase sequences linked to host HLA information dating back to 1979, along with phylogenetically reconstructed HIV-1 sequences dating back to the virus' introduction into North America. Overall, our results support the gradual spread of many—though not all—HIV-1 polymerase immune escape mutations in circulation over time. This is consistent with recent observations from other global regions, though the extent of polymorphism accumulation in North America appears to be lower than in populations with high seroprevalence, older epidemics, and/or limited HLA diversity. Importantly, the risk of acquiring an HIV-1 polymerase sequence at transmission that is substantially preadapted to one's HLA profile remains relatively low in North America, even in the present era.

scholarly journals Fungus Causing White-Nose Syndrome in Bats Accumulates Genetic Variability in North America with No Sign of Recombination

mSphere ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Jigar Trivedi ◽  
Josianne Lachapelle ◽  
Karen J. Vanderwolf ◽  
Vikram Misra ◽  
Craig K. R. Willis ◽  
...  
Keyword(s):  
North America ◽  
North American ◽  
Disease Ecology ◽  
Spontaneous Mutation ◽  
North American Population ◽  
Pseudogymnoascus Destructans ◽  
Clonal Population ◽  
White Nose Syndrome ◽  
The North ◽  
Single Clone

ABSTRACT Emerging fungal diseases of wildlife are on the rise worldwide, and the white-nose syndrome (WNS) epidemic in North American bats is a catastrophic example. The causal agent of WNS is a single clone of the fungus Pseudogymnoascus destructans. Early evolutionary change in this clonal population has major implications for disease ecology and conservation. Accumulation of variation in the fungus through mutation, and shuffling of variation through recombination, could affect the virulence and transmissibility of the fungus and the durability of what appears to be resistance arising in some bat populations. Our genome-wide analysis shows that the clonal population of P. destructans has expanded in size from a single genotype, has begun to accumulate variation through mutation, and presents no evidence as yet of genetic exchange among individuals. IMPORTANCE Since its discovery in 2006, the emerging infectious disease known as white-nose syndrome has killed millions of bats in North America, making it one of the most devastating wildlife epidemics in recorded history. We demonstrate that there has been as yet only spontaneous mutation across the North American population of P. destructans, and we find no indication of recombination. Thus, selective forces, which might otherwise impact pathogenic virulence, have so far had essentially no genetic variation on which to act. Our study confirmed the time of origin for the first and, thus far, only introduction of P. destructans to North America. This system provides an unprecedented opportunity to follow the evolution of a host-pathogen interaction unfolding in real time.

scholarly journals Caver Knowledge and Biosecurity Attitudes Towards White-Nose Syndrome and Implications for Global Spread

EcoHealth ◽  
2021 ◽  
Author(s):  
S. Salleh ◽  
K. Cox-Witton ◽  
Y. Salleh ◽  
Jasmin Hufschmid
Keyword(s):  
Risk Assessment ◽  
North America ◽  
Pseudogymnoascus Destructans ◽  
White Nose Syndrome ◽  
Qualitative Survey ◽  
The World ◽  
Global Spread ◽  
Willingness To Help ◽  
Sydney Australia

AbstractWhite-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has caused catastrophic declines of bat populations in North America. Risk assessment indicates that cavers could pose a risk for the spread of the fungus, however, information on cavers’ knowledge of WNS and their caving and biosecurity habits is lacking. An anonymous qualitative survey was completed by delegates (n = 134) from 23 countries at an international speleological conference in Sydney, Australia. Cavers indicated that they visit caves frequently (80.6% at least bimonthly), including outside of their own country, but 20.3% of respondents did not know about WNS prior to the conference. Some respondents were incorrect, or unsure, about whether they had visited caves in countries where P. destructans occurs (26.5%) or whether their own country was free of the fungus (7.8%). Although 65.9% of respondents were aware of current decontamination protocols, only 23.9% and 31.2% (when in Australian or overseas caves, respectively) fully adhered to them. Overall, cavers showed strong willingness to help prevent further spread of this disease, but further efforts at education and targeted biosecurity activities may be urgently needed to prevent the spread of P. destructans to Australia and to other unaffected regions of the world.

scholarly journals Progressive vowel height harmony in Proto-Kikongo and Proto-Bantu

2019 ◽  
Vol 40 (1) ◽  
pp. 23-73 ◽  
Author(s):  
Heidi Goes ◽  
Koen Bostoen
Keyword(s):  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Long Distance ◽  
Systematic Comparison ◽  
Bantu Languages ◽  
Most Recent Common Ancestor ◽  
Focal Area ◽  
Different Types ◽  
Historical Comparative ◽  
Vowel Height

AbstractThe systematic comparison of the different types of progressive Vowel Height Harmony (pVHH) attested within the Kikongo Language Cluster (KLC) leads to the conclusion that this common Bantu process of long-distance assimilation cannot be reconstructed to Proto-Kikongo. The ‘(a)symmetric-pVHH’ and ‘back-pVHH’ patterns, the two main and structurally different kinds of pVHH within the KLC, emerged independently and relatively late within two distinct subgroups, viz. South Kikongo and North Kikongo respectively. Moreover, the ‘(a)symmetric-pVHH’ pattern further spread from a South Kikongo focal area coinciding with the heartland of the Kongo kingdom to other parts of the KLC through contact-induced dialectal diffusion. Furthermore, the historical-comparative evidence from the KLC suggests that neither symmetric nor asymmetric pVHH should be reconstructed to Proto-Bantu, the most recent common ancestor of all Bantu languages.

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