scholarly journals Complex History of Codiversification and Host Switching of a Newfound Soricid-Borne Orthohantavirus in North America

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 637 ◽  
Author(s):  
Schuyler W. Liphardt ◽  
Hae Ji Kang ◽  
Laurie J. Dizney ◽  
Luis A. Ruedas ◽  
Joseph A. Cook ◽  
...  
Keyword(s):  
North America ◽  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
Population Expansion ◽  
Host Population ◽  
Viral Gene ◽  
Host Switching ◽  
Western North America ◽  
Mitochondrial Cytochrome B ◽  
History Of

Orthohantaviruses are tightly linked to the ecology and evolutionary history of their mammalian hosts. We hypothesized that in regions with dramatic climate shifts throughout the Quaternary, orthohantavirus diversity and evolution are shaped by dynamic host responses to environmental change through processes such as host isolation, host switching, and reassortment. Jemez Springs virus (JMSV), an orthohantavirus harbored by the dusky shrew (Sorex monticola) and five close relatives distributed widely in western North America, was used to test this hypothesis. Total RNAs, extracted from liver or lung tissue from 164 shrews collected from western North America during 1983–2007, were analyzed for orthohantavirus RNA by reverse transcription polymerase chain reaction (RT-PCR). Phylogenies inferred from the L-, M-, and S-segment sequences of 30 JMSV strains were compared with host mitochondrial cytochrome b. Viral clades largely corresponded to host clades, which were primarily structured by geography and were consistent with hypothesized post-glacial expansion. Despite an overall congruence between host and viral gene phylogenies at deeper scales, phylogenetic signals were recovered that also suggested a complex pattern of host switching and at least one reassortment event in the evolutionary history of JMSV. A fundamental understanding of how orthohantaviruses respond to periods of host population expansion, contraction, and secondary host contact is the key to establishing a framework for both more comprehensive understanding of orthohantavirus evolutionary dynamics and broader insights into host–pathogen systems.

Evolutionary history of alpine and subalpineDaphniain western North America

2013 ◽  
Vol 58 (7) ◽  
pp. 1512-1522 ◽  
Author(s):  
Brooks E. Miner ◽  
Roland A. Knapp ◽  
John K. Colbourne ◽  
Michael E. Pfrender
Keyword(s):  
North America ◽  
Evolutionary History ◽  
Western North America ◽  
History Of

Evolutionary history of New World ticks of the genus Dermacentor (Ixodida: Ixodidae), and the origin of D. variabilis

2019 ◽  
Vol 127 (4) ◽  
pp. 863-875 ◽  
Author(s):  
Paula Lado ◽  
Hans Klompen
Keyword(s):  
North America ◽  
Evolutionary History ◽  
New World ◽  
Dermacentor Variabilis ◽  
Eastern North America ◽  
Western North America ◽  
Land Bridge ◽  
Phylogenetic Reconstructions ◽  
History Of ◽  
Migration Event

Abstract This study integrates biogeographical and phylogenetic data to determine the evolutionary history of the New World Dermacentor, and the origin of D. variabilis. The phylogenetic reconstructions presented here strongly support the hypothesis of an Afrotropical origin for Dermacentor, with later dispersal to Eurasia and the Nearctic. Phylogenetic and biogeographical data suggest that the genus reached the New World through the Beringia land bridge, from south-east Asia. The monophyly of the genus is supported, and most of the New World Dermacentor species appear as monophyletic. Dermacentor occidentals constitutes the sister lineage of D. variabilis, and the latter is subdivided into two well-supported clades: an eastern and a western clade. The western clade is genetically more variable than the eastern. The genus Dermacentor probably originated in Africa, and dispersed to the Palearctic and then to the New World through the Beringian route. Dermacentor variabilis appears to have originated in western North America, and then dispersed to eastern North America, probably in a single migration event.

scholarly journals The evolutionary history of a gammaretrovirus currently colonizing the mule deer genome is marked by extensive recombination

2021 ◽  
Author(s):  
Lei Yang ◽  
Raunaq Malhotra ◽  
Rayan Chikhi ◽  
Daniel Elleder ◽  
Theodora Kaiser ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Mule Deer ◽  
Endogenous Retrovirus ◽  
Host Population ◽  
Endogenous Retroviruses ◽  
Genomic Diversity ◽  
Evolutionary Trajectory ◽  
History Of

AbstractBackgroundAll vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although it is clear that endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term co-evolution of ERV and host. Newly colonized ERVs are thought unlikely to contribute to host genome evolution because germline infections are rare and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed.Here we investigate the history of cervid endogenous retrovirus (CrERV) acquisition and expansion in the mule deer genome to determine the potential impact of endogenizing retroviruses on host genomic diversity.MethodsA mule deer genome was de novo assembled from short and long insert mate pair reads. Scaffolds were further assembled using reference assisted chromosome assembly (RACA) to provide spatial orientation of CrERV insertion sites and to facilitate assembly of CrERV sequences. We applied phylogenetic and coalescent approaches to non-recombinant genomes to determine CrERV evolutionary history, augmenting ancestral divergence estimates with the prevalence of each CrERV locus in a population of mule deer. Recombination history was investigated on partial genome alignments.ResultsThe CrERV composition and diversity in the mule deer genome has recently measurably increased by horizontal acquisition of a new retroviruses lineage and because of recombination with existing CrERV. Resulting interlineage recombinants also endogenized and subsequently retrotransposed. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion by retrotransposition of one recombinant CrERV lineage.ConclusionsThere has been a burst of CrERV integrations during a recent retrovirus epizootic that increased genomic CrERV burden and has resulted in extensive insertional polymorphism in contemporary mule deer genomes. Recombination is a defining feature of CrERV evolutionary dynamics driven by this colonization, increasing CrERV burden and CrERV genetic diversity. These data support that retroviral colonization during an epizootic provides a burst of genomic diversity to the host population.

Complex evolutionary history of the pallid dotted-blue butterfly (Lycaenidae: Euphilotes pallescens ) in the Great Basin of western North America

2013 ◽  
Vol 40 (11) ◽  
pp. 2059-2070 ◽  
Author(s):  
Joseph S. Wilson ◽  
Michelle Sneck ◽  
Dennis D. Murphy ◽  
Chris C. Nice ◽  
James A. Fordyce ◽  
...  
Keyword(s):  
North America ◽  
Great Basin ◽  
Evolutionary History ◽  
Western North America ◽  
History Of ◽  
Blue Butterfly ◽  
Complex Evolutionary History

scholarly journals Resolving the Evolutionary History of Campanula (Campanulaceae) in Western North America

PLoS ONE ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. e23559 ◽  
Author(s):  
Barry M. Wendling ◽  
Kurt E. Galbreath ◽  
Eric G. DeChaine
Keyword(s):  
North America ◽  
Evolutionary History ◽  
Western North America ◽  
History Of

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

Signatures of mito-nuclear discordance in Schistosoma turkestanicum indicate a complex evolutionary history of emergence in Europe

Parasitology ◽  
2017 ◽  
Vol 144 (13) ◽  
pp. 1752-1762 ◽  
Author(s):  
SCOTT P. LAWTON ◽  
LAUREN I. BOWEN ◽  
AIDAN M. EMERY ◽  
GÁBOR MAJOROS
Keyword(s):  
Evolutionary History ◽  
Molecular Diversity ◽  
Population Expansion ◽  
Its Sequences ◽  
Cox1 Gene ◽  
Internal Transcribed Spacer Region ◽  
Recent Population Expansion ◽  
Haplotype Frequencies ◽  
History Of ◽  
Low Levels

SUMMARYHigh levels of molecular diversity were identified in mitochondrial cytochrome c oxidase (cox1) gene sequences of Schistosoma turkestanicum from Hungary. These cox1 sequences were all specific to Hungary which contrasted with the low levels of diversity seen in the nuclear internal transcribed spacer region (ITS) sequences, the majority of which were shared between China and Iran isolates. Measures of within and between host molecular variation within S. turkestanicum showed there to be substantial differences in molecular diversity, with cox1 being significantly more diverse than the ITS. Measures of haplotype frequencies revealed that each host contained its own subpopulation of genetically unique parasites with significant levels of differentiation. Pairwise mismatch analysis of cox1 sequences indicated S. turkestanicum populations to have a bimodal pairwise difference distribution and to be stable unlike the ITS sequences, which appeared to have undergone a recent population expansion event. Positive selection was also detected in the cox1 sequences, and biochemical modelling of the resulting protein illustrated significant mutational events causing an alteration to the isoelectric point of the cox1 protein, potentially altering metabolism. The evolutionary signature from the cox1 indicates local adaptation and long establishment of S. turkestanicum in Hungary with continual introgression of nuclear genes from Asian isolates. These processes have led to the occurrence of mito-nuclear discordance in a schistosome population

scholarly journals Evolutionary history of mole rats (genus Nannospalax) inferred from mitochondrial cytochrome b sequence

2011 ◽  
Vol 105 (2) ◽  
pp. 446-455 ◽  
Author(s):  
BORIS KRYŠTUFEK ◽  
ELENA IVANITSKAYA ◽  
ATILLA ARSLAN ◽  
EMINE ARSLAN ◽  
ELENA V. BUŽAN
Keyword(s):  
Cytochrome B ◽  
Evolutionary History ◽  
Mitochondrial Cytochrome ◽  
Mitochondrial Cytochrome B ◽  
History Of
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