Recombination and local population structure of the root endophytic fungus Glutinomyces brunneus based on microsatellite analyses

Lyme disease (LD) is the most common tick-borne human disease in Europe, and Borrelia garinii, which is associated with avian reservoirs, is one of the most genetically diverse and widespread human pathogenic genospecies from the B. burgdorferi sensu lato (s.l.) complex. The clinical manifestations of LD are known to vary between regions and depend on the genetic strain even within Borrelia genospecies. It is thus of importance to explore the genetic diversity of such pathogenic borreliae for the wide range of host and ecological contexts. In this study, multilocus sequence typing (MLST) was employed to investigate the local population structure of B. garinii in Ixodes ricinus ticks. The study took place in a natural wetland in Slovakia, temporally encompassing spring and autumn bird migration periods as well as the breeding period of resident birds. In total, we examined 369 and 255 ticks collected from 78 birds and local vegetation, respectively. B. burgdorferi s.l. was detected in 43.4% (160/369) of ticks recovered from birds and in 26.3% (67/255) of questing ticks, respectively. Considering the ticks from bird hosts, the highest prevalence was found for single infections with B. garinii (22.5%). Infection intensity of B. garinii in bird-feeding ticks was significantly higher than that in questing ticks. We identified ten B. garinii sequence types (STs) occurring exclusively in bird-feeding ticks, two STs occurring exclusively in questing ticks, and one ST (ST 244) occurring in both ticks from birds and questing ticks. Four B. garinii STs were detected for the first time herein. With the exception of ST 93, we detected different STs in spring and summer for bird-feeding ticks. Our results are consistent with previous studies of the low geographic structuring of B. garinii genotypes. However, our study reveals some consistency in local ST occurrence and a geographic signal for one of the clonal complexes.

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Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents

PLoS Genetics ◽

10.1371/journal.pgen.1009269 ◽

2021 ◽

Vol 17 (2) ◽

pp. e1009269

Author(s):

Gerry Tonkin-Hill ◽

Shazia Ruybal-Pesántez ◽

Kathryn E. Tiedje ◽

Virginie Rougeron ◽

Michael F. Duffy ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Population Structure ◽

Surface Antigen ◽

Local Population ◽

Biological Significance ◽

Public Health Problem ◽

Major Public Health Problem ◽

Malaria Surveillance ◽

Geographic Population ◽

Variant Surface Antigen

Malaria remains a major public health problem in many countries. Unlike influenza and HIV, where diversity in immunodominant surface antigens is understood geographically to inform disease surveillance, relatively little is known about the global population structure of PfEMP1, the major variant surface antigen of the malaria parasite Plasmodium falciparum. The complexity of the var multigene family that encodes PfEMP1 and that diversifies by recombination, has so far precluded its use in malaria surveillance. Recent studies have demonstrated that cost-effective deep sequencing of the region of var genes encoding the PfEMP1 DBLα domain and subsequent classification of within host sequences at 96% identity to define unique DBLα types, can reveal structure and strain dynamics within countries. However, to date there has not been a comprehensive comparison of these DBLα types between countries. By leveraging a bioinformatic approach (jumping hidden Markov model) designed specifically for the analysis of recombination within var genes and applying it to a dataset of DBLα types from 10 countries, we are able to describe population structure of DBLα types at the global scale. The sensitivity of the approach allows for the comparison of the global dataset to ape samples of Plasmodium Laverania species. Our analyses show that the evolution of the parasite population emerging out of Africa underlies current patterns of DBLα type diversity. Most importantly, we can distinguish geographic population structure within Africa between Gabon and Ghana in West Africa and Uganda in East Africa. Our evolutionary findings have translational implications in the context of globalization. Firstly, DBLα type diversity can provide a simple diagnostic framework for geographic surveillance of the rapidly evolving transmission dynamics of P. falciparum. It can also inform efforts to understand the presence or absence of global, regional and local population immunity to major surface antigen variants. Additionally, we identify a number of highly conserved DBLα types that are present globally that may be of biological significance and warrant further characterization.

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Life histories predict genetic diversity and population structure within three species of Octopus targeted by small-scale fisheries in Northwest Mexico

10.7287/peerj.preprints.3016 ◽

2017 ◽

Author(s):

José F Domínguez-Contreras ◽

Adrian Munguia-Vega ◽

Bertha P Ceballos-Vázquez ◽

Marcial Arellano-Martínez ◽

Francisco J García-Rodríguez ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Size ◽

Effective Population Size ◽

Gulf Of California ◽

Life Histories ◽

Local Population ◽

Small Scale ◽

Effective Population ◽

Northwest Mexico

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species with varying life histories targeted by artisanal fisheries in the region, lack of information about the distribution of each species and metapopulation size and structure could impede effective fisheries management to avoid overexploitation. Here we tested if different life histories in three species of octopus help to predict observed patterns of genetic diversity, population dynamics, structure and connectivity that could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the Pacific coast of the Baja California peninsula. We tested four a priori hypothesis derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We found that the species with low fecundity and without a planktonic larval stage (Octopus bimaculoides) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, suggesting limited dispersal and high local recruitment. In contrast, two species with higher fecundity and planktonic larvae (O. bimaculatus, O. hubbsorum) showed higher effective population size and genetic diversity, and overall lower kinship and population structure, supporting higher levels of gene flow over a larger geographical scale. Even among the latter, there were differences in the calculated parameters possibly associated with increased connectivity in the species with the longest planktonic larval duration (O. bimaculatus). We consider that O. bimaculoides could be more susceptible to over exploitation of small, isolated populations that could have longer recovery times, and suggest that management should take place within each local population. For the two species with pelagic larvae, management should consider metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal between localities driven by ocean currents. The distribution of each species and variations in their reproductive timing should also be considered when establishing marine reserves or seasonal fishing closures.

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Population structure of the dusky pipefish (Syngnathus floridae) from the Atlantic and Gulf of Mexico, as revealed by mitochondrial DNA and microsatellite analyses

Journal of Biogeography ◽

10.1111/j.1365-2699.2010.02288.x ◽

2010 ◽

Vol 37 (7) ◽

pp. 1363-1377 ◽

Cited By ~ 19

Author(s):

Kenyon B. Mobley ◽

Clayton M. Small ◽

Nathaniel K. Jue ◽

Adam G. Jones

Keyword(s):

Mitochondrial Dna ◽

Population Structure ◽

Gulf Of Mexico ◽

Syngnathus Floridae ◽

Microsatellite Analyses

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Local population structure ofHymenoscyphus fraxineussurveyed by an enlarged set of microsatellite markers

Forest Pathology ◽

10.1111/efp.12185 ◽

2015 ◽

Vol 45 (5) ◽

pp. 400-407 ◽

Cited By ~ 8

Author(s):

Z. Haňáčková ◽

O. Koukol ◽

L. Havrdová ◽

A. Gross

Keyword(s):

Population Structure ◽

Microsatellite Markers ◽

Local Population

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Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus

Royal Society Open Science ◽

10.1098/rsos.171532 ◽

2018 ◽

Vol 5 (5) ◽

pp. 171532 ◽

Cited By ~ 1

Author(s):

Joaquin C. B. Nunez ◽

Leann M. Biancani ◽

Patrick A. Flight ◽

Diane E. Nacci ◽

David M. Rand ◽

...

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Fundulus Heteroclitus ◽

Isolation By Distance ◽

Spatial Scales ◽

Purifying Selection ◽

Spatial Distance ◽

Estuarine Fish ◽

Synonymous Mutations ◽

Microsatellite Analyses

Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in N e and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade.

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Local Population Structure and Patterns of Western Hemisphere Dispersal forCoccidioidesspp., the Fungal Cause of Valley Fever

mBio ◽

10.1128/mbio.00550-16 ◽

2016 ◽

Vol 7 (2) ◽

Cited By ~ 43

Author(s):

David M. Engelthaler ◽

Chandler C. Roe ◽

Crystal M. Hepp ◽

Marcus Teixeira ◽

Elizabeth M. Driebe ◽

...

Keyword(s):

Population Structure ◽

South America ◽

Population Genomics ◽

Local Population ◽

The United States ◽

Western Hemisphere ◽

Phylogeographic Structure ◽

High Morbidity ◽

Valley Fever ◽

Desert Southwest

ABSTRACTCoccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species,Coccidioides immitisandC. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure inC. posadasiiand demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number ofC. immitisstrains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated thatC. posadasiiis the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin forC. posadasiiand describe a pathway for dispersal and distribution out of this region.IMPORTANCECoccidioidomycosis, or valley fever, is caused by the pathogenic fungiCoccidioides posadasiiandC. immitis. The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement ofC. posadasiifrom North America to South America. Here we comparatively analyze eighty-six genomes of the twoCoccidioidesspecies and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations ofC. posadasii.

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Dutch population structure across space, time and GWAS design

Nature Communications ◽

10.1038/s41467-020-18418-4 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Ross P. Byrne ◽

◽

Wouter van Rheenen ◽

Leonard H. van den Berg ◽

Jan H. Veldink ◽

...

Keyword(s):

Population Structure ◽

The Netherlands ◽

Middle Ages ◽

Local Population ◽

Restricted Gene Flow ◽

Single Nucleotide ◽

Fine Grained ◽

Genome Wide ◽

External Reference ◽

International Data

Abstract Previous genetic studies have identified local population structure within the Netherlands; however their resolution is limited by use of unlinked markers and absence of external reference data. Here we apply advanced haplotype sharing methods (ChromoPainter/fineSTRUCTURE) to study fine-grained population genetic structure and demographic change across the Netherlands using genome-wide single nucleotide polymorphism data (1,626 individuals) with associated geography (1,422 individuals). We identify 40 haplotypic clusters exhibiting strong north/south variation and fine-scale differentiation within provinces. Clustering is tied to country-wide ancestry gradients from neighbouring lands and to locally restricted gene flow across major Dutch rivers. North-south structure is temporally stable, with west-east differentiation more transient, potentially influenced by migrations during the middle ages. Despite superexponential population growth, regional demographic estimates reveal population crashes contemporaneous with the Black Death. Within Dutch and international data, GWAS incorporating fine-grained haplotypic covariates are less confounded than standard methods.

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