scholarly journals Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

2021 ◽  
Vol 17 (8) ◽  
pp. e1009287
Author(s):  
Jason A. Hendry ◽  
Dominic Kwiatkowski ◽  
Gil McVean
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Genetic Data ◽  
Parasite Prevalence ◽  
Epidemiological Models ◽  
Related Factors ◽  
Malaria Epidemiology ◽  
Moran Model ◽  
Classical Models ◽  
Parasite Evolution

There is an abundance of malaria genetic data being collected from the field, yet using these data to understand the drivers of regional epidemiology remains a challenge. A key issue is the lack of models that relate parasite genetic diversity to epidemiological parameters. Classical models in population genetics characterize changes in genetic diversity in relation to demographic parameters, but fail to account for the unique features of the malaria life cycle. In contrast, epidemiological models, such as the Ross-Macdonald model, capture malaria transmission dynamics but do not consider genetics. Here, we have developed an integrated model encompassing both parasite evolution and regional epidemiology. We achieve this by combining the Ross-Macdonald model with an intra-host continuous-time Moran model, thus explicitly representing the evolution of individual parasite genomes in a traditional epidemiological framework. Implemented as a stochastic simulation, we use the model to explore relationships between measures of parasite genetic diversity and parasite prevalence, a widely-used metric of transmission intensity. First, we explore how varying parasite prevalence influences genetic diversity at equilibrium. We find that multiple genetic diversity statistics are correlated with prevalence, but the strength of the relationships depends on whether variation in prevalence is driven by host- or vector-related factors. Next, we assess the responsiveness of a variety of statistics to malaria control interventions, finding that those related to mixed infections respond quickly (∼months) whereas other statistics, such as nucleotide diversity, may take decades to respond. These findings provide insights into the opportunities and challenges associated with using genetic data to monitor malaria epidemiology.

scholarly journals Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

2020 ◽  
Author(s):  
Jason A. Hendry ◽  
Dominic Kwiatkowski ◽  
Gil McVean
Keyword(s):  
Genetic Diversity ◽  
Malaria Control ◽  
Focal Point ◽  
Genetic Data ◽  
Parasite Prevalence ◽  
Malaria Surveillance ◽  
Related Factors ◽  
Malaria Epidemiology ◽  
Moran Model ◽  
Classical Models

AbstractThere is an abundance of malaria genetic data being collected from the field, yet using this data to understand features of regional epidemiology remains a challenge. A key issue is the lack of models that relate parasite genetic diversity to epidemiological parameters. Classical models in population genetics characterize changes in genetic diversity in relation to demographic parameters, but fail to account for the unique features of the malaria life cycle. In contrast, epidemiological models, such as the Ross-Macdonald model, capture malaria transmission dynamics but do not consider genetics. Here, we have developed an integrated model encompassing both parasite evolution and regional epidemiology. We achieve this by combining the Ross-Macdonald model with an intra-host continuous-time Moran model, thus explicitly representing the evolution of individual parasite genomes in a traditional epidemiological framework. Implemented as a stochastic simulation, we use the model to explore relationships between measures of parasite genetic diversity and parasite prevalence, a widely-used metric of transmission intensity. First, we explore how varying parasite prevalence influences genetic diversity at equilibrium. We find that multiple genetic diversity statistics are correlated with prevalence, but the strength of the relationships depends on whether variation in prevalence is driven by host- or vector-related factors. Next, we assess the responsiveness of a variety of statistics to malaria control interventions, finding that those related to mixed infections respond quickly (~ months) whereas other statistics, such as nucleotide diversity, may take decades to respond. These findings provide insights into the opportunities and challenges associated with using genetic data to monitor malaria epidemiology.Author summaryKnowledge of how the prevalence of P.falciparum malaria varies, either between regions or through time, is critical to the operation of malaria control programs. Yet obtaining this information through traditional methods is fraught with challenges. Parasite genetic data is increasingly accessible, and may provide an alternative means to estimate P.falciparum prevalence in the field. However, our understanding of how the genetic diversity of parasite populations relates to prevalence is limited, and suitable models to guide our understanding are largely lacking. Here, we merge two classical models – the Ross-Macondald and the Moran – to produce a framework in which the relationships between parasite genetic diversity and prevalence can be explored. We find that several genetic diversity statistics are correlated with prevalence, although to differing degrees, and over different time scales. Overall, statistics related to mixed infection are robustly and rapidly responsive to changes in prevalence, suggesting they may be a useful focal point for the development of malaria surveillance methods that harness genetic data.

scholarly journals Modelling homogeneous regions of social vulnerability to malaria in Rwanda

2016 ◽  
Vol 11 (1s) ◽  
Author(s):  
Jean Pierre Bizimana ◽  
Stefan Kienberger ◽  
Michael Hagenlocher ◽  
Emmanuel Twarabamenye
Keyword(s):  
Social Vulnerability ◽  
Socioeconomic Development ◽  
Malaria Incidence ◽  
Spatially Explicit ◽  
Related Factors ◽  
Remote Areas ◽  
Malaria Epidemiology ◽  
Vulnerability Indicators ◽  
Applied Approach ◽  
Homogeneous Regions

Despite the decline in malaria incidence due to intense interventions, potentials for malaria transmission persist in Rwanda. To eradicate malaria in Rwanda, strategies need to expand beyond approaches that focus solely on malaria epidemiology and also consider the socioeconomic, demographic and biological/disease-related factors that determine the vulnerability of potentially exposed populations. This paper analyses current levels of social vulnerability to malaria in Rwanda by integrating a set of weighted vulnerability indicators. The paper uses regionalisation techniques as a spatially explicit approach for delineating homogeneous regions of social vulnerability to malaria. This overcomes the limitations of administrative boundaries for modelling the trans-boundary social vulnerability to malaria. The utilised approach revealed high levels of social vulnerability to malaria in the highland areas of Rwanda, as well as in remote areas where populations are more susceptible. Susceptibility may be due to the populations’ lacking the capacity to anticipate mosquito bites, or lacking resilience to cope with or recover from malaria infection. By highlighting the most influential indicators of social vulnerability to malaria, the applied approach indicates which vulnerability domains need to be addressed, and where appropriate interventions are most required. Interventions to improve the socioeconomic development in highly vulnerable areas could prove highly effective, and provide sustainable outcomes against malaria in Rwanda. This would ultimately increase the resilience of the population and their capacity to better anticipate, cope with, and recover from possible infection.

scholarly journals Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
ABDUL BASITH ◽  
Abinawanto Abinawanto ◽  
ENI KUSRINI ◽  
YASMAN YASMAN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Phylogenetic Reconstruction ◽  
Partial Sequence ◽  
Diversity Analysis ◽  
Epinephelus Coioides ◽  
Substitution Model ◽  
Genetic Diversity Analysis

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

VNTR typing of the bacterial rice pathogen Burkholderia glumae reveals the coexistence of several diverging lineages in a single field in Colombia.

Plant Disease ◽  
2021 ◽  
Author(s):  
Gilles Bena ◽  
Paola Fory ◽  
Johanna Echeverri ◽  
Gloria Mosquera
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Tandem Repeats ◽  
Genetic Relationships ◽  
Rice Paddy ◽  
Rice Cultivar ◽  
Bacterial Strains ◽  
Burkholderia Glumae ◽  
Significant Drop ◽  
Origin And Evolution

Bulkholderia glumae is responsible for the panicle blight disease of rice. This disease is present worldwide and can result in significant drop in yields. In order to estimate the genetic diversity of the bacterial strains present in a rice paddy field in Colombia, we sampled 109 strains from infected panicles. In order to detect fine genetic relationships among related haplotypes, and to overcome a very low nucleotide diversity detected in previous studies, we designed primers to amplify and sequence several highly variable minisatellite loci, or Variable Number Tandem Repeats, as well as part of the Toxoflavin toxA gene, in all strains. Results show that (i) the toxA nucleotide diversity defined four lineages and was similar to that detected in several fields in Japan, (ii) data suggest that B. glumae has spread from Asia to America without major loss of genetic diversity, (iii) five VNTR loci discriminated the strains within the field revealing single and multi-infections of the rice panicles with a wide distribution of the haplotypes among the different plots. Even though disease levels vary considerably from year to year, the bacterial genetic diversity is maintained within a field. We do not detect any geographical structuring within the field, nor any effect of the rice cultivar on the observed diversity. The consequences on the origin and evolution of the bacteria are discussed.

scholarly journals Coalescent Theory of Migration Network Motifs

2019 ◽  
Vol 36 (10) ◽  
pp. 2358-2374
Author(s):  
Nicolas Alcala ◽  
Amy Goldberg ◽  
Uma Ramakrishnan ◽  
Noah A Rosenberg
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Nucleotide Diversity ◽  
Natural Populations ◽  
Node Degree ◽  
Small Subset ◽  
Network Motifs ◽  
Coalescent Theory ◽  
Migration Networks ◽  
The Impact

Abstract Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a high mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with low density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into disconnected components. We illustrate our results using two example data sets—sky island birds of genus Sholicola and Indian tigers—identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity, and they can assist in designing strategies to alter population migration networks toward maximizing genetic variation in the context of conservation of endangered species.

scholarly journals Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 306
Author(s):  
Maurizio Rossetto ◽  
Peter D. Wilson ◽  
Jason Bragg ◽  
Joel Cohen ◽  
Monica Fahey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
A Priori ◽  
Genetic Data ◽  
Environmental Data ◽  
Specific Data ◽  
Acacia Species ◽  
Simple Observation ◽  
Source Plant ◽  
Species Specific

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.

Conservation genetics of Pitcher’s thistle (Cirsium pitcheri), an endangered Great Lakes endemic

Botany ◽  
2010 ◽  
Vol 88 (3) ◽  
pp. 250-257 ◽  
Author(s):  
Martha Gauthier ◽  
Emily Crowe ◽  
Lindsey Hawke ◽  
Neil Emery ◽  
Paul Wilson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Great Lakes ◽  
Genetic Data ◽  
Nuclear Data ◽  
Population Connectivity ◽  
Chloroplast Microsatellite ◽  
Management Plans ◽  
Low Levels ◽  
Cirsium Pitcheri ◽  
Pitcher's Thistle

Pitcher's thistle ( Cirsium pitcheri Torr. ex Eaton (Torr. & Gray)) is a Great Lakes endemic that in Canada is designated as threatened at both the provincial (Ontario) and national levels. Management plans will benefit from conservation genetic data, which can provide insight into population genetic diversity and differentiation. We obtained genetic data from nuclear and chloroplast microsatellite markers from 17 populations of C. pitcheri around the Great Lakes. The nuclear data revealed overall low levels of diversity, high levels of inbreeding, and low levels of population connectivity. The chloroplast data identified a single haplotype, which is consistent with reduced genetic diversity following postglacial colonization. The high levels of inbreeding within populations will likely pose a serious threat to populations in the short term; these have resulted from a combination of low connectivity between populations, and small and fluctuating population sizes. Future management of C. pitcheri populations should consider human-mediated dispersal of plants or seeds among sites.

scholarly journals Prevalence, hematological findings and genetic diversity ofBartonellaspp. in domestic cats from Valdivia, Southern Chile

Parasitology ◽  
2016 ◽  
Vol 144 (6) ◽  
pp. 773-782 ◽  
Author(s):  
ANANDA MÜLLER ◽  
ROMINA WALKER ◽  
PEDRO BITTENCOURT ◽  
ROSANGELA ZACARIAS MACHADO ◽  
JYAN LUCAS BENEVENUTE ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Complete Blood Count ◽  
Bartonella Henselae ◽  
Hematological Parameters ◽  
Species Differentiation ◽  
Southern Chile ◽  
Domestic Cats ◽  
Real Time Quantitative Pcr ◽  
First Time

SUMMARYThe present study determined the prevalence, hematological findings and genetic diversity ofBartonellaspp. in domestic cats from Valdivia, Southern Chile. A complete blood count andnuoGgene real-time quantitative PCR (qPCR) forBartonellaspp. were performed in 370 blood samples from cats in Valdivia, Southern Chile.nuoGqPCR-positive samples were submitted to conventional PCR for thegltAgene and sequencing for species differentiation and phylogenetic analysis. Alignment ofgltAgene was used to calculate the nucleotide diversity, polymorphic level, number of variable sites and average number of nucleotide differences.BartonellaDNA prevalence in cats was 18·1% (67/370). Twenty-nine samples were sequenced with 62·0% (18/29) identified asBartonella henselae, 34·4% (10/29) asBartonella clarridgeiae, and 3·4% (1/29) asBartonella koehlerae. Bartonella-positive cats had low DNA bacterial loads and their hematological parameters varied minimally. EachBartonellaspecies from Chile clustered together and with otherBartonellaspp. described in cats worldwide.Bartonella henselaeandB. clarridgeiaeshowed a low number of variable sites, haplotypes and nucleotide diversity.Bartonella clarridgeiaeandB. koehleraeare reported for the first time in cats from Chile and South America, respectively.

scholarly journals Variation in reproductive effort, genetic diversity and mating systems across Posidonia australis seagrass meadows in Western Australia

AoB Plants ◽  
2020 ◽  
Vol 12 (4) ◽  
Author(s):  
Elizabeth A Sinclair ◽  
Jane M Edgeloe ◽  
Janet M Anthony ◽  
John Statton ◽  
Martin F Breed ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating System ◽  
Western Australia ◽  
Reproductive Effort ◽  
Genetic Data ◽  
Fruit Production ◽  
Mixed Mating ◽  
Mixed Mating System ◽  
Shark Bay ◽  
Range Edge

Abstract Populations at the edges of their geographical range tend to have lower genetic diversity, smaller effective population sizes and limited connectivity relative to centre of range populations. Range edge populations are also likely to be better adapted to more extreme conditions for future survival and resilience in warming environments. However, they may also be most at risk of extinction from changing climate. We compare reproductive and genetic data of the temperate seagrass, Posidonia australis on the west coast of Australia. Measures of reproductive effort (flowering and fruit production and seed to ovule ratios) and estimates of genetic diversity and mating patterns (nuclear microsatellite DNA loci) were used to assess sexual reproduction in northern range edge (low latitude, elevated salinities, Shark Bay World Heritage Site) and centre of range (mid-latitude, oceanic salinity, Perth metropolitan waters) meadows in Western Australia. Flower and fruit production were highly variable among meadows and there was no significant relationship between seed to ovule ratio and clonal diversity. However, Shark Bay meadows were two orders of magnitude less fecund than those in Perth metropolitan waters. Shark Bay meadows were characterized by significantly lower levels of genetic diversity and a mixed mating system relative to meadows in Perth metropolitan waters, which had high genetic diversity and a completely outcrossed mating system. The combination of reproductive and genetic data showed overall lower sexual productivity in Shark Bay meadows relative to Perth metropolitan waters. The mixed mating system is likely driven by a combination of local environmental conditions and pollen limitation. These results indicate that seagrass restoration in Shark Bay may benefit from sourcing plant material from multiple reproductive meadows to increase outcrossed pollen availability and seed production for natural recruitment.

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