Find research datasets worth reusing

Genetic anaylsis of pediatric osteoarticular infections

Background: Pediatric osteoarticular infections are commonly caused by Staphylococcus aureus. The contribution of S. aureus genomic variability to pathogenesis of these infections is poorly described. Methods: We prospectively enrolled 47 children over 3 1/2 years from whom S. aureus was isolated on culture---12 uninfected with skin colonization, 16 with skin abscesses, 19 with osteoarticular infections (four with septic arthritis, three with acute osteomyelitis, six with acute osteomyelitis and septic arthritis and six with chronic osteomyelitis). Isolates underwent whole genome sequencing, with assessment for 254 virulence genes and any mutations as well as the creation of a phylogenetic tree. Finally, isolates were compared for their ability to form static biofilms and compared to the genetic analysis. Results: No sequence types predominated amongst osteoarticular infections. Only genes involved in the evasion of host immune defenses were more frequently carried by isolates from osteoarticular infections than from skin colonization (p=.02). Virulence gene mutations were only noted in 14 genes (three regulating biofilm formation) when comparing isolates from subjects with osteoarticular infections and those with skin colonization. Biofilm results demonstrated large heterogeneity in the isolates' capacity to form static biofilms, with healthy control isolates producing more robust biofilm formation. Conclusions: S. aureus causing osteoarticular infections are genetically heterogeneous, and more frequently harbor genes involved in immune evasion than less invasive isolates. However, virulence gene carriage overall is similar with infrequent mutations, suggesting that pathogenesis of S. aureus osteoarticular infections may be primarily regulated at transcriptional and/or translational levels.

Summary data for plots in: Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations

Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting in local extinction and recolonization through evolving dispersal, facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favour increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.

opencc-by-4.0Aug 2022View details →

Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda

This data repository contains the raw data used in the morphological analyses for "Morphological and genetic mechanisms underlying the plasticity of the coral Porites astreoides across depths in Bermuda"  <ul> <li><a href="http://dx.doi.org/10.1016/j.jsb.2023.108036" target="_blank" rel="noopener">10.1016/j.jsb.2023.108036</a></li> </ul>

Raw data: Association and functional analysis of angiotensin-converting enzyme 2 gene genetic variants with the pathogenesis of pre-eclampsia

These data were generated to investigate the association and functional analysis of angiotensin-converting enzyme 2 genetic variants with the pathogenesis of pre-eclampsia(PE). This study conducted a case-control study involving 327 PE patients and 591 healthy pregnant women to explore the associations between candidate variants in the ACE2 gene variants and the pathogenesis of PE.This study collected clinical samples and data, and used logistic regression, false positive report rate, multi factor dimension reduction, functional analysis and other analysis methods to process the research data. Potential functional ACE2 gene variants (rs2106809 A>G, rs6632677 G>C, and rs2074192 C>T) were selected and genotyped using kompetitive allele-specific PCR. The strength of the associations between the studied genetic variants and the risk of PE were evaluated using odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Finally,it showed that the rs2106809 A>Gis significantly associated with the risk of PE via individual locus effects and/or complex gene-gene and gene-environment interactions.

Data from: Resident-disperser differences and genetic variability affect communities in microcosms

Dispersal is a key process mediating ecological and evolutionary dynamics. Its effects on the dynamics of spatially-structured systems, population genetics, or species range distribution can depend on phenotypic differences between dispersing and non-dispersing individuals. However, scaling up the importance of resident-disperser differences to communities and ecosystems has rarely been considered, in spite of intraspecific phenotypic variability being an important factor mediating community structure and productivity. Here, we used the ciliate Tetrahymena thermophila, in which phenotypic traits are known to differ between residents and dispersers, to test (i) whether these resident-disperser differences affect biomass and composition in competitive communities composed of four other Tetrahymena species, and (ii) whether these effects are genotype-dependent. We found that dispersers led to lower community biomass compared to residents. This effect was highly consistent across the twenty T. thermophila genotypes used, despite intraspecific variability in resident-disperser phenotypic differences. We also found a significant genotypic effect on biomass production, showing that intraspecific variability has consequences for communities. Our study suggests that individual dispersal strategy can scale up to community productivity in a predictable way, opening new perspectives to the functioning of spatially structured ecosystems.

Genetic response to human‐induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway

Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; i.e. Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant FST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbour-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (FST) between marine and brackish sprat is larger in the comparison Norway- Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, i.e., 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.

A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component

Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis. This archive contains genetic variation data derived from genome sequencing of 580 bumblebee samples collected from high-elevation locations in Colorado. The species are Bombus sylvicola (n=214), Bombus balteatus (n=299) and "incognitus" (n=67).

Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden

The Eurasian spruce bark beetle, Ips typographus, is a major pest, capable of killing spruce forests during large population outbreaks. Recorded dispersal distances of individual beetles are typically within hundreds of meters or a few kilometres. However, the connectivity between populations at larger distances and longer time spans and how this is affected by the habitat is less studied, despite its importance for understanding at which distances local outbreaks may spread. Previous population genetic studies in I. typographus typically used low resolution markers. Here, we use genome-wide data to assess population structure and connectivity of I. typographus in Sweden. We used 152 individuals from 19 population samples, distributed over 830 km from Strömsund (63º 46' 8'' N) in the north to Nyteboda (56º 8' 50'' N) in the south, to capture processes at a large regional scale, and a transect sampling design adjacent to a recent outbreak to capture processes at a smaller scale (76 km). Using restriction site-associated DNA sequencing (RADseq) markers capturing 1409-1997 SNPs throughout the genome, we document a weak genetic structure over the large scale, potentially indicative of high connectivity with extensive gene flow. No differentiation was detected at the smaller scale. We find indications of isolation-by-distance both for relative (FST) and absolute divergence (Dxy). The two northernmost populations are most differentiated from the remaining populations, and diverge in parallel to the southern populations for a set of outlier loci. In conclusion, the population structure of I. typographus in Sweden is weak, suggesting a high capacity to disperse and establish outbreak populations in new territories.

Data and supplementary materials from: Large genetic divergence underpins cryptic local adaptation across ecological and evolutionary gradients

Environmentally covarying local adaptation is a form of cryptic local adaptation in which the covariance of the genetic and environmental effects on a phenotype obscures the divergence between locally adapted genotypes. Here, we systematically document the magnitude and drivers of the genetic effect (VG) for two forms of environmentally covarying local adaptation: counter- and cogradient variation. Using a hierarchical Bayesian meta-analysis, we calculated the overall effect size of VG as 1.05 and 2.13 for populations exhibiting countergradient or cogradient variation, respectively. These results indicate that the genetic contribution to phenotypic variation represents a 1.05 to 2.13 standard deviation change in trait value between the most disparate populations depending on if populations are expressing counter- or cogradient variation. We also found that while there was substantial variance among abiotic and biotic covariates, the covariates with the largest mean effects were temperature (2.41) and gamete size (2.81). Our results demonstrate the pervasiveness and large genetic effects underlying environmentally covarying local adaptation in wild populations and highlights the importance of accounting for these effects in future studies.

Data from: Genetic patterns of Magnolia in the Lesser Antilles: Stepwise colonisation leading to highly inbred island 'populations'

Aim: Test for genetic signatures of island biogeographic patterns, using a slowly evolving, recent colonist with a low dispersal capability in an island chain without linear chronosequence; evaluate the multiple-endemic status of the species; and quantify genetic diversity of extant island populations. Location: The Lesser Antilles (Caribbean). Taxon: Magnolia dodecapetala (Magnoliaceae). Methods: Genetic diversity was characterised using Sanger sequencing of 21 individuals amplified for 11 DNA markers, plus microsatellite data of 195 individuals genotyped with 19 simple sequence repeat (SSR) markers. Sanger sequencing data were used to construct a Bayesian phylogenetic hypothesis, while SSR markers were used to run approximate Bayesian computation (ABC) demographic analyses and calculate population statistics. Results: Both types of molecular data support stepwise colonization, decoupled from known island ages. The ABC analyses support a north to south migration while the Sanger sequencing data indicates a mixture of island progression rule and stepping stone dispersal. The SSR data show strong genetic structuring per island and significant inbreeding in all populations except in Saint Lucia. The lowest genetic diversity is found in the population from Saint Vincent. A high amount of genetic linkage occurs in a subpopulation from Dominica. Main conclusions: Biogeographic patterns for the complex geological setting of the Lesser Antilles are uncovered using a slowly evolving study species. All genetic data support treating each island as distinct Management Units for conservation and call for a re-evaluation of the species limits. Inbreeding threatens the survival of island populations and the populations of Saint Vincent and Dominica represent conservation priorities.

Pollinator data from: Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs

In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species (Polygonatum multiflorum (L.) All. and Anemone nemorosa L.) in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1763) and the hoverfly Melanostoma scalare (Fabricus, 1794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest-associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.

Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees

Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well characterized. However, there is no consensus on the biological processes underlying these patterns, and multiple competing hypotheses have been proposed, several of which center on climatic stability. Here, we ask if Late Quaternary climatic stability predicts contemporary population structure and genomic-level diversity in two palm species: Syagrus botryophora and S. pseudococos (Arecaceae) We first use species occurrence data to model the distribution of suitable environments in 62 time-slice climate projections over the last 120 thousand years, and summarize stability over that period. We then use >25,000 RADseq-generated SNPs to i) describe the spatial patterns of genomic variation in both species, ii) test how well genomic variation is explained by isolation by distance and by the environmental resistance imposed by historical instability (isolation by resistance) and iii) test for a correlation between genetic diversity and historical stability. The contemporary range of S. botryophora has been relatively stable over the last 30 thousand years and there are two isolated regions of high stability for S. pseudococos. The genomic data recovers a clear pattern of isolation by distance in S. botryophora and two structured populations in S. pseudococos. Consequently, the contribution of isolation by resistance to overall genetic structure is much higher in S. pseudococos. Genetic diversity is not significantly correlated with historical stability in either species. Based on the concordance between historical stability and genetic structure, Late Quaternary climate stability may have maintained population connectivity within S. botryophora and promoted intraspecific divergence in S. pseudococos. Conversely, historical stability does not seem to be driving spatial patterns of genetic diversity. This study supports the primary role of climatic stability in determining spatial population structure, but not genetic diversity, in the Atlantic Forest.

opencc-by-4.0Sep 2022View details →

Dataset: A phase field model combined with genetic algorithm for polycrystalline hafnium zirconium oxide ferroelectrics

The folder includes generated data MATLAB scripts to read/plot the polarization-electric field (PE) hysteresis curves. The dataset contains phase field generated polycrystalline grain structure, simulated domain structures during polarization reversal, and symmetric PE curves (measured and simulated). Polycrystalline grain structures: The output files are in the *.txt format, readable by MTEX to generate orientation maps. Column(1)       Column(2)       Column(3)       Column(4)       Column(5)    X                Y             φ(rad)          θ(rad)          𝜓(rad)   ...              ...             ...             ...             ...   ...              ...             ...             ...             ...   ...              ...             ...             ...             ... Domain structures: The output files are in the *.csv format, which can be visualized by programs like ParaView. Column(1)       Column(2)       Column(3)       Column(4)    X                Y               Z               P   ...              ...             ...             ...   ...              ...             ...             ...   ...              ...             ...             ... PE curves: The output files are in the *.txt format, readable by MATLAB. Column(1)       Column(2) E(MV/cm)        P(μC/cm²)   ...              ...   ...              ...   ...              ... List of datasets:- Fig. 1: pecurves/calib_func1.txt (Calibrated p(e)), pecurves/measpe_hf50.txt (Measured PE curve), pecurves/simpe_calib.txt (Simulated PE curve). Fig. 2(a): polcr_struc/xy_col.txt (XY top view), polcr_struc/yz_col.txt (YZ side view), polcr_struc/xz_col.txt (ZX side view) Fig. 2(b): pecurves/simpe_gaopt.txt (Simulated PE curve), pecurves/measpe_hf50.txt (Measured PE curve). Fig. 3: pecurves/calib_func.txt (Calibrated p(e)), pecurves/gaopt_func.txt (GA optimized p(e)). Fig. 5: pecurves/simpe_gaopt.txt (Case 1), pecurves/simpe_elast.txt (Case 2). Fig. 4(e): dom_struc/dom_profile1.csv, (f) dom_struc/dom_profile2.csv, (g) dom_struc/dom_profile3.csv, (h) dom_struc/dom_profile4.csv, (m) dom_struc/dom_profile5.csv, (n) dom_struc/dom_profile6.csv, (o) dom_struc/dom_profile7.csv, (p) dom_struc/dom_profile8.csv Fig. 6: pecurves/simpe_gaopt.txt (GA fit coefficients), pecurves/simpe_ldc1.txt (Set 1), pecurves/simpe_ldc2.txt (Set 2). Fig. 7(a): pecurves/simpe_gaopt.txt (𝝂₀ = 1.0), pecurves/simpe_fr80.txt (𝝂₀ = 0.8), pecurves/simpe_fr50.txt (𝝂₀ = 0.5). Fig. 7(b): pecurves/measpe_hf50.txt (Hf₀.₅Zr₀.₅O₂), pecurves/measpe_hf75.txt (Hf₀.₇₅Zr₀.₂₅O₂). Fig. 8: pecurves/simpe_fr38.txt (Simulated PE curve), pecurves/measpe_hf75.txt (Measured PE curve). Fig. 9: pecurves/simpe_gaopt.txt (Random non-textured), pecurves/simpe_tex001.txt ([001] fiber textured), pecurves/simpe_tex111.txt ([111] fiber textured). Fig. 10(a): polcr_struc/xy_equ.txt (XY top view), polcr_struc/yz_equ.txt (YZ side view), polcr_struc/xz_equ.txt (ZX side view) Fig. 10(b): pecurves/simpe_colmor.txt (Columnar grain microstructure), pecurves/simpe_equmor.txt (Equiaxed grain microstructure). List of MATLAB scripts: Fig 1: matlab_scripts/fig1.m Fig 2(b): matlab_scripts/fig2b.m Fig 3: matlab_scripts/fig3.m Fig 5: matlab_scripts/fig5.m Fig 6: matlab_scripts/fig6.m Fig 7(a): matlab_scripts/fig7a.m Fig 7(b): matlab_scripts/fig7b.m Fig 8: matlab_scripts/fig8.m Fig 9: matlab_scripts/fig9.m Fig 10(b): matlab_scripts/fig10b.m

Data from: Extra-pair paternity correlates with genetic diversity, but not breeding density, in a Neotropical passerine, the Black Catbird

The frequency of extra-pair paternity (EPP) varies widely across socially monogamous birds, but the proximate mechanisms driving this variation remain unclear. In this study, we tested two major factors hypothesized to influence extra-pair mating—breeding density and genetic diversity—by comparing genetic mating patterns in two populations of black catbirds Melanoptila glabrirostris. This Neotropical songbird is endemic to the Yucatán Peninsula, including eastern Mexico, and its offshore islands. We sampled one mainland (Sian Ka'an Biosphere Reserve) and one island (Isla Cozumel) population and used single-nucleotide polymorphisms (SNPs) to quantify heterozygosity and genetic parentage over two breeding seasons. Moderate levels of EPP occurred in both populations (9.5 – 35% of offspring and 17 – 45% of nests). Contrary to predictions, breeding density did not affect EPP: although breeding densities were much higher on the mainland than on the island, EPP rates did not differ between populations, and local breeding density was not correlated with EPP at individual nests. In contrast, partial support emerged for the hypothesis that genetic diversity influences EPP: extra-pair offspring were more heterozygous than within-pair offspring. However, the two populations did not differ in genetic diversity, and neither the heterozygosity of social fathers nor within-pair relatedness predicted EPP. These results are consistent with recent comparative studies suggesting that breeding density is not a critical driver of EPP rates, and that not all tropical songbirds exhibit low rates of EPP.

Genetic data from: Cryptic persistence and loss of local endemism in Lake Constance charr subject to anthropogenic disturbance

Habitat restoration can help to protect and support endangered species. Following the restoration of Lake Constance to oligotrophic conditions, deep-water charr (originally described as Salvelinus profundus Schillinger, 1901) were rediscovered after more than 40 years of presumed extinction caused by eutrophication. Subsequent targeted surveys lead to the capture of a further 127 deep-water charr and 233 sympatric normal charr, Salvelinus cf. umbla. Given a history of intensive stocking in the lake and the possibility of introgressive hybridization, a discussion arose about the genetic status and future conservation strategies of both forms. The current study gathered life history traits and morphological and population genomic data for both extant forms, for comparison with 60–120 years' worth of historical data and museum specimens. The extant deep-water charr resembled historical specimens in terms of body shape, but significant differences between historical and extant normal charr included a decline in gill raker number over time and distinctly different body shapes and growth patterns. RAD-based population genomic analyses of the contemporary samples support these results, revealing the two extant forms to be highly divergent, albeit with a few putative hybrids. SNPs-based population assignment tests of historical and contemporary samples strongly suggest that deep-water charr persisted unaltered in Lake Constance during the eutrophic phase. Meanwhile, none of the historical genomic samples could be assigned to the extant normal S. cf. umbla population. Functional analyses of gill raker number and stocking intensity pointed to stocking with non-endemic charr as the most likely reason for the disappearance of the endemic normal form. These results show that interplay between different anthropogenic impacts, i.e. eutrophication and stocking can lead to irreversible but hard-to-detect impacts on endemic biodiversity. Understanding these impacts is a prerequisite for effective conservation of endangered populations of cryptic fish.

Data from: Are genetic variation and demographic performance linked?

Quantifying the empirical relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. Here, we present eight years of historical demographic data from five populations of Boechera fecunda (Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λS) and extinction risk of each population. We combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, genetics and demography are not strongly correlated, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than more genetically diverse populations. Interestingly, however, a contemporary re-census revealed that, among these populations, genetic rather than demographic parameters were better predictors of current population density, with populations harboring greater genetic diversity maintaining denser populations at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of B. fecunda rather than alternatives such as translocations or reintroductions.

opencc-by-4.0Dec 2021View details →

Dataset for "Genetic diversity and population structure of a wide Pisum spp. core collection."

Silico-DArT and SNP datasets of the IAS pea core collection. Each file contain key information of the molecular markers used to establish the population structure and genetic diversity of the IAs pea core collection.

Population genetic structure of the gastropod species Bulinus truncatus

Background: Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge on their distribution and population dynamics increases our understanding of processes driving disease transmission. This is the first study using High Throughput Sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17 to 150 km) and an inter-regional (1,000 – 5,400 km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively. Methods: Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end Genotyping by Sequencing (GBS) library, comprising of 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections and Single Nucleotide Polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and to construct phylogenetic trees of Bulinus truncatus. Results: A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission. Conclusions: HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of schistosome intermediate host snails and the role of snail species in parasite transmission.

opencc-by-4.0Jun 2022View details →

Characterization data for the manuscript: "Using genetic algorithms to systematically improve the synthesis conditions of Al-PMOF"

Visualize the data in this dataset: <a href="https://www.c6h6.org/zenodo/record/?id=7186602">open entry</a>.