scholarly journals Population genomics ofCryptococcus neoformansvar.grubiireveals new biogeographic relationships and finely maps hybridization

2017 ◽  
Author(s):  
Johanna Rhodes ◽  
Christopher A. Desjardins ◽  
Sean M. Sykes ◽  
Mathew A. Beale ◽  
Mathieu Vanhove ◽  
...  
Keyword(s):  
South America ◽  
Cryptococcus Neoformans ◽  
Fungal Pathogen ◽  
Population Genomics ◽  
Natural Populations ◽  
Sub Saharan Africa ◽  
Large Set ◽  
Serotype A ◽  
Sub Saharan ◽  
Genetic Substructure

AbstractCryptococcus neoformansvar.grubiiis the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them. While most isolates ofC. neoformansvar.grubiibelong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates ofC. neoformansvar.grubii (serotype A/A) and of hybrids withC. neoformansvar.neoformans(serotype A/D) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil revealed that the previously ‘African’ VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions demonstrating the highly dispersive nature of this pathogen.Author SummaryCryptococcus neoformansvar.grubiiis a human fungal pathogen of immunocompromised individuals that has global clinical impact, causing half a million deaths per year. Substantial genetic substructure exists for this pathogen, with two lineages found globally (VNI, VNII) whereas a third has appeared confined to sub-Saharan Africa (VNB). Here, we utilized genome sequencing of a large set of global isolates to examine the genetic diversity, hybridization, and biogeography of these lineages. We found that while the three major lineages are well separated, recombination between the lineages has occurred, notably resulting in hybrid isolates with segmented ancestry across the genome. In addition, we showed that isolates from South America are placed within the VNB lineage, formerly thought to be confined to Africa, and that there is phylogenetic separation between these geographies that substantially expands the diversity of these lineages. Our findings provide a new framework for further studies of the dynamics of natural populations ofC. neoformansvar.grubii.

scholarly journals A population genomics approach to assessing the genetic basis of within-host microevolution underlying recurrent cryptococcal meningitis infection

2016 ◽  
Author(s):  
Johanna Rhodes ◽  
Mathew A. Beale ◽  
Mathieu Vanhove ◽  
Joseph N. Jarvis ◽  
Shichina Kannambath ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Cryptococcal Meningitis ◽  
Genetic Basis ◽  
Population Genomics ◽  
Antifungal Drugs ◽  
Sub Saharan Africa ◽  
Gene Encoding ◽  
Nonsense Mutations ◽  
Before And After ◽  
Sub Saharan

AbstractRecurrence of meningitis due toCryptococcus neoformansafter treatment causes substantial mortality in HIV/AIDS patients across sub-Saharan Africa. In order to determine whether recurrence occurred due to relapse of the original infecting isolate or reinfection with a different isolate weeks or months after initial treatment, we used whole-genome sequencing to assess the genetic basis of infection in 17 HIV-infected individuals with recurrent cryptococcal meningitis. Comparisons revealed a clonal relationship for 15 pairs of isolates recovered before and after recurrence showing relapse of the original infection. The two remaining pairs showed high levels of genetic heterogeneity; in one pair we found this to be a result of infection by mixed genotypes, whilst the second was a result of nonsense mutations in the gene encoding the DNA mismatch repair proteinsMSH2, MSH5andRAD5. These nonsense mutations led to a hypermutator state, leading to dramatically elevated rates of synonymous and non-synonymous substitutions. Hypermutator phenotypes owing to nonsense mutations in these genes have not previously been reported inCryptococcus neoformansand represent a novel pathway for rapid within-host adaptation and evolution of resistance to firstline antifungal drugs.

Genetic polymorphism and population structure ofEchinococcus ortleppi

Parasitology ◽  
2016 ◽  
Vol 144 (4) ◽  
pp. 450-458 ◽  
Author(s):  
F. ADDY ◽  
M. WASSERMANN ◽  
F. BANDA ◽  
H. MBAYA ◽  
J. ASCHENBORN ◽  
...  
Keyword(s):  
Genetic Polymorphism ◽  
South America ◽  
Southern Africa ◽  
Dna Sequences ◽  
Intraspecific Variability ◽  
Sensu Stricto ◽  
Sub Saharan Africa ◽  
Geographical Regions ◽  
Sub Saharan ◽  
Eastern And Southern Africa

SUMMARYThe zoonotic cestodeEchinococcus ortleppi(Lopez-Neyra and Soler Planas, 1943) is mainly transmitted between dogs and cattle. It occurs worldwide but is only found sporadically in most regions, with the notable exception of parts of southern Africa and South America. Its epidemiology is little understood and the extent of intraspecific variability is unknown. We have analysed in the present study the genetic diversity among 178E. ortleppiisolates from sub-Saharan Africa, Europe and South America using the complete mitochondrialcox1(1608 bp) andnad1(894 bp) DNA sequences. Genetic polymorphism within the loci revealed 15cox1and sixnad1haplotypes, respectively, and 20 haplotypes of the concatenated genes. Presence of most haplotypes was correlated to geographical regions, and only one haplotype had a wider spread in both eastern and southern Africa. Intraspecific microvariance was low in comparison withEchinococcus granulosussensu stricto, despite the wide geographic range of examined isolates. In addition, the various sub-populations showed only subtle deviation from neutrality and were mostly genetically differentiated. This is the first insight into the population genetics of the enigmatic cattle adaptedEchinococcus ortleppi. It, therefore, provides baseline data for biogeographical comparison amongE. ortleppiendemic regions and for tracing its translocation paths.

Comparative gene genealogical analyses of strains of serotype AD identify recombination in populations of serotypes A and D in the human pathogenic yeast Cryptococcus neoformans

Microbiology ◽  
2003 ◽  
Vol 149 (8) ◽  
pp. 2147-2154 ◽  
Author(s):  
Jianping Xu ◽  
Thomas G. Mitchell
Keyword(s):  
Monoclonal Antibodies ◽  
Cryptococcus Neoformans ◽  
Natural Populations ◽  
The Other ◽  
Pathogenic Yeast ◽  
Gene Genealogy ◽  
Serotype A ◽  
The World ◽  
Significant Divergence ◽  
Allelic Group

Cryptococcus neoformans is a major pathogen of humans throughout the world. Using commercial monoclonal antibodies to capsular epitopes, strains of C. neoformans manifest five serotypes: A, B, C, D and AD. Previous studies demonstrated significant divergence among serotypes A, B, C and D, which are typically haploid. In contrast, most strains of serotype AD are diploid or aneuploid and result from recent hybridization between strains of serotypes A and D. Whether serotypes A, B, C and D represent strictly asexual lineages is not known. Using comparative genealogical analyses of two genes, the authors investigated whether recombination occurred among strains within serotypes A and D. For each of 14 serotype AD strains, a portion (642 bp) of the orotidine monophosphate pyrophosphorylase (URA5) gene was cloned and sequenced. Each of these 14 strains contained two different alleles and sequences for both alleles were obtained. The URA5 gene genealogy was compared to that derived from the laccase (LAC) gene, which was reported recently for the same 14 strains. For both genes, each of the 14 serotype AD strains contained two phylogenetically distinct alleles: one allele was highly similar to those from serotype A strains and the other to alleles from serotype D strains. However, within both the serotype A allelic group and the serotype D allelic group, there was significant incongruence between genealogies derived from URA5 and LAC. The results suggest recombination in natural populations of both serotypes A and D.

scholarly journals Biomass burning fuel consumption dynamics in the tropics and subtropics assessed from satellite

2016 ◽  
Vol 13 (12) ◽  
pp. 3717-3734 ◽  
Author(s):  
Niels Andela ◽  
Guido R. van der Werf ◽  
Johannes W. Kaiser ◽  
Thijs T. van Leeuwen ◽  
Martin J. Wooster ◽  
...  
Keyword(s):  
South America ◽  
Fuel Consumption ◽  
Spatial Patterns ◽  
Field Measurements ◽  
Sub Saharan Africa ◽  
Burned Area ◽  
Return Periods ◽  
Sub Saharan ◽  
In Fire ◽  
Consumption Dynamics

Abstract. Landscape fires occur on a large scale in (sub)tropical savannas and grasslands, affecting ecosystem dynamics, regional air quality and concentrations of atmospheric trace gasses. Fuel consumption per unit of area burned is an important but poorly constrained parameter in fire emission modelling. We combined satellite-derived burned area with fire radiative power (FRP) data to derive fuel consumption estimates for land cover types with low tree cover in South America, Sub-Saharan Africa, and Australia. We developed a new approach to estimate fuel consumption, based on FRP data from the polar-orbiting Moderate Resolution Imaging Spectroradiometer (MODIS) and the geostationary Spinning Enhanced Visible and Infrared Imager (SEVIRI) in combination with MODIS burned-area estimates. The fuel consumption estimates based on the geostationary and polar-orbiting instruments showed good agreement in terms of spatial patterns. We used field measurements of fuel consumption to constrain our results, but the large variation in fuel consumption in both space and time complicated this comparison and absolute fuel consumption estimates remained more uncertain. Spatial patterns in fuel consumption could be partly explained by vegetation productivity and fire return periods. In South America, most fires occurred in savannas with relatively long fire return periods, resulting in comparatively high fuel consumption as opposed to the more frequently burning savannas in Sub-Saharan Africa. Strikingly, we found the infrequently burning interior of Australia to have higher fuel consumption than the more productive but frequently burning savannas in northern Australia. Vegetation type also played an important role in explaining the distribution of fuel consumption, by affecting both fuel build-up rates and fire return periods. Hummock grasslands, which were responsible for a large share of Australian biomass burning, showed larger fuel build-up rates than equally productive grasslands in Africa, although this effect might have been partially driven by the presence of grazers in Africa or differences in landscape management. Finally, land management in the form of deforestation and agriculture also considerably affected fuel consumption regionally. We conclude that combining FRP and burned-area estimates, calibrated against field measurements, is a promising approach in deriving quantitative estimates of fuel consumption. Satellite-derived fuel consumption estimates may both challenge our current understanding of spatiotemporal fuel consumption dynamics and serve as reference datasets to improve biogeochemical modelling approaches. Future field studies especially designed to validate satellite-based products, or airborne remote sensing, may further improve confidence in the absolute fuel consumption estimates which are quickly becoming the weakest link in fire emission estimates.

scholarly journals Structure of Dark Triad Dirty Dozen Across Eight World Regions

Assessment ◽  
2020 ◽  
pp. 107319112092261
Author(s):  
Radosław Rogoza ◽  
Magdalena Żemojtel-Piotrowska ◽  
Peter K. Jonason ◽  
Jarosław Piotrowski ◽  
Keith W. Campbell ◽  
...  
Keyword(s):  
South America ◽  
Measurement Invariance ◽  
Western Europe ◽  
Dark Triad ◽  
Sub Saharan Africa ◽  
The Past ◽  
World Regions ◽  
Dirty Dozen ◽  
The Difference ◽  
Sub Saharan

The Dark Triad (i.e., narcissism, psychopathy, Machiavellianism) has garnered intense attention over the past 15 years. We examined the structure of these traits’ measure—the Dark Triad Dirty Dozen (DTDD)—in a sample of 11,488 participants from three W.E.I.R.D. (i.e., North America, Oceania, Western Europe) and five non-W.E.I.R.D. (i.e., Asia, Middle East, non-Western Europe, South America, sub-Saharan Africa) world regions. The results confirmed the measurement invariance of the DTDD across participants’ sex in all world regions, with men scoring higher than women on all traits (except for psychopathy in Asia, where the difference was not significant). We found evidence for metric (and partial scalar) measurement invariance within and between W.E.I.R.D. and non-W.E.I.R.D. world regions. The results generally support the structure of the DTDD.

Identifying threatened species in the "south" using new criteria

1998 ◽  
Vol 4 (1) ◽  
pp. 33 ◽  
Author(s):  
A. J. Stattersfield
Keyword(s):  
South America ◽  
Threatened Species ◽  
Pacific Islands ◽  
Numerical Data ◽  
Sub Saharan Africa ◽  
Conservation Action ◽  
Red Lists ◽  
Sub Saharan ◽  
New Criteria ◽  
Clear Objective

The first application of the new IUCN threatened species categories to birds is reviewed. The advantage of this system is that it is characterized by clear, objective, quantitative criteria. However, for many species, requisite numerical data are lacking, and the magnitude of potential threats has to be inferred. Numbers of threatened species are compared for South America, sub-Saharan Africa, and Indo-Pacific Islands. Further analysis identifies the most important countries in terms of priority for conservation action for threatened species, the key habitats for their survival and the main dangers faced. The changes between successive Red Lists indicate a possible extinction crisis of considerable magnitude, whereby half the world's birds could disappear in 800 years. Averting this crisis requires identifying and protecting sites where suites of threatened species co-occur.

scholarly journals Evidence of Sexual Recombination amongCryptococcus neoformansSerotype A Isolates in Sub-Saharan Africa

2003 ◽  
Vol 2 (6) ◽  
pp. 1162-1168 ◽  
Author(s):  
Anastasia P. Litvintseva ◽  
Robert E. Marra ◽  
Kirsten Nielsen ◽  
Joseph Heitman ◽  
Rytas Vilgalys ◽  
...  
Keyword(s):  
Population Genetic ◽  
Clonal Expansion ◽  
Sub Saharan Africa ◽  
Direct Impact ◽  
Common Cause ◽  
Serotype A ◽  
Fungal Meningitis ◽  
Sexual Recombination ◽  
Sub Saharan ◽  
Bipolar Mating System

The most common cause of fungal meningitis in humans,Cryptococcus neoformansserotype A, is a basidiomycetous yeast with a bipolar mating system. However, the vast majority (>99.9%) ofC. neoformansserotype A isolates possess only one of the two mating type alleles (MATα). Isolates with the other allele (MATa) were recently discovered and proven to mate in the laboratory. It has been a mystery whether and whereC. neoformansstrains undergo sexual reproduction. Here, we applied population genetic approaches to demonstrate that a population ofC. neoformansserotype A clinical isolates from Botswana contains an unprecedented proportion of fertileMATa isolates and exhibits evidence of both clonal expansion and recombination within two partially genetically isolated subgroups. Our findings provide evidence for sexual recombination among some populations ofC. neoformansserotype A from sub-Saharan Africa, which may have a direct impact on their evolution.

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