Search Results: geneology

Genomics Recapitulates History in Europe

dx.plos.org/10.1371/journal.pbio.1001556

Transmission Pathways of Foot-and-Mouth Disease Virus in the United Kingdom in 2007

dx.plos.org/10.1371/journal.ppat.1000050
Foot-and-mouth disease (FMD) virus causes an acute vesicular disease of domesticated and wild ruminants and pigs. Identifying sources of FMD outbreaks is often confounded by incomplete epidemiological evidence and the numerous routes by which virus can spread (movements of infected animals or their products, contaminated persons, objects, and aerosols). Here, we show that the outbreaks of FMD in the United Kingdom in August 2007 were caused by a derivative of FMDV O1 BFS 1860, a virus ...

Rapid Strategy for Screening by Pyrosequencing of Influenza Virus Reassortants - Candidates for Live Attenuated Vaccines

dx.plos.org/10.1371/journal.pone.0092580
Background: Live attenuated influenza vaccine viruses (LAIVs) can be generated by classical reassortment of gene segments between a cold adapted, temperature sensitive and attenuated Master Donor Virus (MDV) and a seasonal wild-type (wt) virus. The vaccine candidates contain hemagglutinin (HA) and neuraminidase (NA) genes derived from the circulating wt viruses and the remaining six genes derived from the MDV strains. Rapid, efficient selection of the viruses with 6∶2 genome composit...

Two New Species of Liuixalus (Rhacophoridae, Anura): Evidence from Morphological and Molecular Analyses

dx.plos.org/10.1371/journal.pone.0136134
Due to small body sizes, superficial similarities in morphologies, and obscure activity behaviors, the phylogeny and taxonomy of species in the genus Liuixalus were very troublesome. Some species might comprise a complex of cryptic species. To investigate the species of group, we constructed the matrilineal genealogy of the genus using 16s rRNA mitochondrial DNA sequences. Analyses recovered six well supported matrilines that involved L. romeri, L. ocellatus, L. hainanus, L. calcarius...

Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans

dx.plos.org/10.1371/journal.pgen.1006560
The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong ...

Operationalising Factors That Explain the Emergence of Infectious Diseases: A Case Study of the Human Campylobacteriosis Epidemic

dx.plos.org/10.1371/journal.pone.0079331
A framework of general factors for infectious disease emergence was made operational for Campylobacter utilising explanatory variables including time series and risk factor data. These variables were generated using a combination of empirical epidemiology, case-case and case-control studies, time series analysis, and microbial sub-typing (source attribution, diversity, genetic distance) to unravel the changing/emerging aetiology of human campylobacteriosis. The study focused on Scotla...

Adaptive Evolution of Mus Apobec3 Includes Retroviral Insertion and Positive Selection at Two Clusters of Residues Flanking the Substrate Groove

dx.plos.org/10.1371/journal.ppat.1000974
Mouse APOBEC3 (mA3) is a cytidine deaminase with antiviral activity. mA3 is linked to the Rfv3 virus resistance factor, a gene responsible for recovery from infection by Friend murine leukemia virus, and mA3 allelic variants differ in their ability to restrict mouse mammary tumor virus. We sequenced mA3 genes from 38 inbred strains and wild mouse species, and compared the mouse sequence and predicted structure with human APOBEC3G (hA3G). An inserted sequence was identified in the viru...

Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes

dx.plos.org/10.1371/journal.pone.0131435
Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the “climatic niche”); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness an...

Fifteen into Three Does Go: Morphology, Genetics and Genitalia Confirm Taxonomic Inflation of New Zealand Beetles (Chrysomelidae: Eucolaspis)

dx.plos.org/10.1371/journal.pone.0143258
Eucolaspis Sharp 1886 is a New Zealand native leaf beetle genus (Coleoptera: Chrysomelidae: Eumolpinae) with poorly described species and a complex taxonomy. Many economically important fruit crops are severely damaged by these beetles. Uncertain species taxonomy of Eucolaspis is leaving any biological research, as well as pest management, tenuous. We used morphometrics, mitochondrial DNA and male genitalia to study phylogenetic and geographic diversity of Eucolaspis in New Zealand. F...

SnIPRE: Selection Inference Using a Poisson Random Effects Model

dx.plos.org/10.1371/journal.pcbi.1002806
We present an approach for identifying genes under natural selection using polymorphism and divergence data from synonymous and non-synonymous sites within genes. A generalized linear mixed model is used to model the genome-wide variability among categories of mutations and estimate its functional consequence. We demonstrate how the model's estimated fixed and random effects can be used to identify genes under selection. The parameter estimates from our generalized linear mode...

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