Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. ...Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geographic area in Japan and additionally identified putative environmental drivers and their effect on co-existing multiple stonefly species. Double-digest restriction-associated DNA (ddRAD) libraries were independently sequenced for 219 individuals from 23 sites across four geographical regions along a nationwide latitudinal gradient in Japan.
A total of 4251 candidate single nucleotide polymorphisms (SNPs) strongly associated with local adaptation were discovered using Latent mixed models; of these, 294 SNPs showed strong correlation with environmental variables, specifically precipitation and altitude, using distance-based redundancy analysis. Genome-genome comparison among the seven species revealed a high sequence similarity of candidate SNPs within a geographical region, suggesting the occurrence of a parallel evolution process.
Our results revealed genomic signatures of local adaptation and their influence on multiple, co-occurring species. These results can be potentially applied for future studies on river management and climatic stressor impacts.
•DNA metabarcoding identified stream macroinvertebrates mostly at the species level.•Sequence read and sample abundance were significantly correlated.•Most taxa missed by DNA metabarcoding had low ...representation in the community sample.•Predicting variables showed significant variability for DNA metabarcoding.
Conventional morphology-based identification is commonly used for routine assessment of freshwater ecosystems. However, cost and time efficient techniques such as high-throughput sequencing (HTS) based approaches may resolve the constraints encountered in conducting morphology-based surveys. Here, we characterized stream macroinvertebrate species diversity and community composition via metabarcoding and morphological analysis from environmental samples collected from the Shigenobu River Basin in Ehime Prefecture, Japan. We compared diversity metrics and assessed both approaches’ ability to evaluate the relationship between macroinvertebrate community and environmental variables. In total, we morphologically identified 45 taxa (3 families, six subfamilies, 31 genera, and five species) from 8,276 collected individuals from ten study sites. We detected 44 species by metabarcoding, with 35 species collapsed into 11 groups matching the morphologically identified taxa. A significant positive correlation between logged depth (number of HTS reads) and abundance of morphological taxa was observed, which implied that quantitative data could be used for subsequent analyses. We recovered a considerably high rate of relative abundance detection of the morphologically identified samples. Recovery of samples by incidence or presence/absence count were considerably low, with a high rate of false-negative detection specifically for species with scarce representation in the community sample. Given the low taxonomic resolution of the morphological assignment in this study, we report that metabarcoding does not reflect the majority of the species naturally occurring in our site, which could further be proven by performing refined morphological assessment of the samples. However, abundance-based detection proved to be efficient with 92% of the individuals correctly demonstrated. We conclude that DNA metabarcoding provides a practical and cost-effective approach especially for rapid biological monitoring of freshwater macroinvertebrate communities, but further improvements in the detection of scarce samples should be considered to increase the sensitivity of detecting most, if not all, of the species present in the environment.
The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical ...history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times-based on three molecular clock node calibrations-using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades-that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.
Sequential membrane filtration as a pre-processing step for capturing sediment-associated microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient ...temperatures before community profiling through culture-independent molecular techniques. However, the effects of sample pre-processing via filtration on DNA-based profiling of sediment-associated microbial community diversity and composition are poorly understood. Specifically, the influences of pre-processing on the quality and quantity of extracted DNA, high-throughput DNA sequencing reads, and detected microbial taxa need further evaluation.
We assessed the impact of pre-processing freshwater sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size) for 16S rRNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the qualities and quantities of extracted DNA and PCR amplicons, and the read abundance after bioinformatics processing (i.e., denoising and chimeric-read filtering steps) between the two methods. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods' absolute read abundance. More so, at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition.
Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.
Background Insecticide-treated mosquito bed nets and indoor residual spraying are widely used for malaria vector control. However, their effectiveness can be affected by household members’ habits, ...requiring alternative approaches toward malaria vector control. Objective To assess the effectiveness of modified houses in preventing mosquito entry; to assess the impact of house modifications on indoor air conditions and evaluate the acceptability of modified houses in the community where the study was conducted. Methods Five traditional and five modified houses were constructed in Nampula district, Mozambique and underwent a 90-day overnight indoor mosquito collection using Centers for Disease Control and nitride ultraviolet light traps during the rainy season. Mosquitoes were identified morphologically. Indoor temperature, relative humidity, carbon dioxide levels and wind speed were also collected. The Student’s t -test was used to compare the means of the number of mosquitos and environmental factors between both house types. A binomial form of the Generalized Linear Model identified the factors associated with the community volunteer’s preference for house type. Results Modified houses reduced the number of Anopheles by an average of 14.97 mosquitos (95% CI, 11.38–18.56, p < 0.000) and non- Anopheles by 16.66 mosquitoes (95% CI, 8.23–25.09, p < 0.000). Although fewer mosquitoes were trapped in modified houses compared to traditional ones, the modifications were more effective against Anopheles (94% reduction) than for non- Anopheles (71% reduction). The average temperature increased at 0.25°C in modified houses but was not statistically significant (95% CI, −0.62 to 0.12, p = 0.181). Community volunteers preferred modified houses due to reduced mosquito buzzing. The efficacy of modified houses including its acceptability by community, highlight its potential to lower malaria risk. Effective integration of modified houses into the vector control strategy will require raising awareness among communities about malaria risks associated with house structure and training them to modify their houses.
Freshwater biodiversity undergoes degradation due to climate change. Researchers have inferred the effects of climate change on neutral genetic diversity, assuming the fixed spatial distributions of ...alleles. However, the adaptive genetic evolution of populations that may change the spatial distribution of allele frequencies along environmental gradients (i.e., evolutionary rescue) have largely been overlooked. We developed a modeling approach that projects the comparatively adaptive and neutral genetic diversities of four stream insects, using empirical neutral/ putative adaptive loci, ecological niche models (ENMs), and a distributed hydrological-thermal simulation at a temperate catchment under climate change. The hydrothermal model was used to generate hydraulic and thermal variables (e.g., annual current velocity and water temperature) at the present and the climatic change conditions, projected based on the eight general circulation models and the three representative concentration pathways scenarios for the two future periods (2031–2050, near future; 2081–2100, far future). The hydraulic and thermal variables were used for predictor variables of the ENMs and adaptive genetic modeling based on machine learning approaches. The increases in annual water temperature in the near- (+0.3–0.7 °C) and far-future (+0.4–3.2 °C) were projected. Of the studied species, with different ecologies and habitat ranges, Ephemera japonica (Ephemeroptera) was projected to lose rear-edge habitats (i.e., downstream) but retain the adaptive genetic diversity owing to evolutionary rescue. In contrast, the habitat range of the upstream-dwelling Hydropsyche albicephala (Trichoptera) was found to remarkably decline, resulting in decreases in the watershed genetic diversity. While the other two Trichoptera species expanded their habitat ranges, the genetic structures were homogenized over the watershed and experienced moderate decreases in gamma diversity. The findings emphasize the evolutionary rescue potential, depending on the extent of species-specific local adaptation.
Display omitted
•Adaptive process was considered to project genetic diversity under climate change.•A hydrologic model projected future increase in stream temperature up to 3.2 °C.•A mayfly species lost partial habitats but retained genetic diversity.•Caddisfly species gain new habitats but experienced genetic homogenization.•Considering adaptation potentials is central to safeguarding genetic diversity.
Dengue is an endemic vector-borne disease influenced by environmental factors such as landscape and climate. Previous studies separately assessed the effects of landscape and climate factors on ...mosquito occurrence and dengue incidence. However, both factors concurrently coexist in time and space and can interact, affecting mosquito development and dengue disease transmission. For example, eggs laid in a suitable environment can hatch after being submerged in rain water. It has been difficult for conventional statistical modeling approaches to demonstrate these combined influences due to mathematical constraints.
To investigate the combined influences of landscape and climate factors on mosquito occurrence and dengue incidence.
Entomological, epidemiological, and landscape data from the rainy season (July–December) were obtained from respective government agencies in Metropolitan Manila, Philippines, from 2012 to 2014. Temperature, precipitation and vegetation data were obtained through remote sensing. A random forest algorithm was used to select the landscape and climate variables. Afterward, using the identified key variables, a model-based (MOB) recursive partitioning was implemented to test the combined influences of landscape and climate factors on ovitrap index (vector mosquito occurrence) and dengue incidence.
The MOB recursive partitioning for ovitrap index indicated a high sensitivity of vector mosquito occurrence on environmental conditions generated by a combination of high residential density areas with low precipitation. Moreover, the MOB recursive partitioning indicated high sensitivity of dengue incidence to the effects of precipitation in areas with high proportions of residential density and commercial areas.
Dengue dynamics are not solely influenced by individual effects of either climate or landscape, but rather by their synergistic or combined effects. The presented findings have the potential to target vector surveillance in areas identified as suitable for mosquito occurrence under specific climatic conditions and may be relevant as part of urban planning strategies to control dengue.
Display omitted
•Dengue dynamics are influenced by the combined effects of precipitation and landscape.•Landscape factors are strongly influential in increasing the sensitivity of mosquito occurrence.•Climate factors strongly increase the sensitivity of dengue incidence.
Using a stable isotope two- and three-source mixing model, we evaluated trophic contributions of reservoir-derived plankton, epilithon, and terrestrial leaves to stream macroinvertebrates at two dam ...upstream and four dam outlet reaches. We compared four different habitat types co-occurring within the reaches: lotic habitat, bar-head lentic habitat, bar-tail lentic habitat, and isolated pond on sandy bars. Filter-feeders, which provide the highest trophic contributions of reservoir-derived plankton, did not significantly differ among habitats, whereas collector-gatherers and predators differed significantly. Thus, the three-source model analysis for collector-gatherers and predators indicated a lower proportion of reservoir-derived plankton in lentic habitat than in lotic habitat. This difference in food source composition was reflected in the lower trophic contribution of plankton to lentic species. Macroinvertebrates in lentic habitats fed on sources less mixed with reservoir-derived plankton; therefore, the trophic impact of reservoirs was indistinctive at the community level, indicating that lentic habitats can function as trophic refugia to mitigate the trophic impact of reservoirs. Our findings demonstrate that habitat heterogeneity potentially provides a foundation for determining the trophic contribution of food webs while affecting communities when there is anthropogenic input of food resources to the habitat.
Marine bacteria are possible reservoirs of antibiotic-resistance genes (ARGs) originating not only from clinical and terrestrial hot spots but also from the marine environment. We report here for the ...first time a higher rate of the sulfonamide-resistance gene
sul4
in marine bacterial isolates compared with other
sul
genes. Among four sulfonamide-resistance genes (
sul1
,
sul2
,
sul3
, and
sul4
),
sul4
was most abundant (45%) in 74 sulfonamide-resistant marine isolates by PCR screening. The order of abundance was
sul4
(33 isolates)
>sul2
(6 isolates)
>sul3
(5 isolates)
>sul1
(1 isolate). Whole-genome sequencing of 23 isolates of
sul4
-expressing α- and γ-proteobacteria and bacilli revealed that
sul4
was not accompanied by known mobile genetic elements. This suggests that
sul4
in these marine isolates is clonally transferred and not horizontally transferable. Folate metabolism genes formed a cluster with
sul4
, suggesting that the cluster area plays a role in folate metabolism, at which
sul4
functions as a dihydropteroate synthase. Thus,
sul4
might be expressed in marine species and function in folate synthesis, but it is not a transferable ARG.
Stream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect ...communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities. We sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial
cox1
and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and assemblage composition by quantifing the contribution of each reach and habitat to the overall DNA-species diversity using an additive partition analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering could lead to the co-occurrence of DNA-species using a two-step analysis to detect a phylogenetic signal. All four reaches significantly contributed to DNA-species richness, with the meandering reach having the highest contribution. Habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly assemblage possibly due to the high habitat heterogeneity. Among the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This assemblage structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species. Our study shows the importance of different habitats for the spatial and phylogenetic structure of stonefly assemblage and sheds light on the habitat-specific diversity that may help improve conservation practices.
PDF
