Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors

Roman Wenne; Małgorzata Zbawicka; Lis Bach; Petr Strelkov; Mikhail Gantsevich; Piotr Kukliński; Tomasz Kijewski; John H. McDonald; Kristil Kindem Sundsaasen; Mariann Árnyasi; Sigbjørn Lien; Ants Kaasik; Kristjan Herkül; Jonne Kotta

doi:10.3390/genes11050530

Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors

Genes ◽

10.3390/genes11050530 ◽

2020 ◽

Vol 11 (5) ◽

pp. 530 ◽

Cited By ~ 4

Author(s):

Roman Wenne ◽

Małgorzata Zbawicka ◽

Lis Bach ◽

Petr Strelkov ◽

Mikhail Gantsevich ◽

...

Keyword(s):

Environmental Factors ◽

Genetic Variability ◽

Chlorophyll A ◽

Environmental Conditions ◽

Environmental Variables ◽

Ice Cover ◽

Allele Frequencies ◽

Environmental Drivers ◽

Single Nucleotide ◽

Mixed Populations

Large-scale climate changes influence the geographic distribution of biodiversity. Many taxa have been reported to extend or reduce their geographic range, move poleward or displace other species. However, for closely related species that can hybridize in the natural environment, displacement is not the only effect of changes of environmental variables. Another option is subtler, hidden expansion, which can be found using genetic methods only. The marine blue mussels Mytilus are known to change their geographic distribution despite being sessile animals. In addition to natural dissemination at larval phase—enhanced by intentional or accidental introductions and rafting—they can spread through hybridization and introgression with local congeners, which can create mixed populations sustaining in environmental conditions that are marginal for pure taxa. The Mytilus species have a wide distribution in coastal regions of the Northern and Southern Hemisphere. In this study, we investigated the inter-regional genetic differentiation of the Mytilus species complex at 53 locations in the North Atlantic and adjacent Arctic waters and linked this genetic variability to key local environmental drivers. Of seventy-nine candidate single nucleotide polymorphisms (SNPs), all samples were successfully genotyped with a subset of 54 SNPs. There was a clear interregional separation of Mytilus species. However, all three Mytilus species hybridized in the contact area and created hybrid zones with mixed populations. Boosted regression trees (BRT) models showed that inter-regional variability was important in many allele models but did not prevail over variability in local environmental factors. Local environmental variables described over 40% of variability in about 30% of the allele frequencies of Mytilus spp. For the 30% of alleles, variability in their frequencies was only weakly coupled with local environmental conditions. For most studied alleles the linkages between environmental drivers and the genetic variability of Mytilus spp. were random in respect to “coding” and “non-coding” regions. An analysis of the subset of data involving functional genes only showed that two SNPs at Hsp70 and ATPase genes correlated with environmental variables. Total predictive ability of the highest performing models (r2 between 0.550 and 0.801) were for alleles that discriminated most effectively M. trossulus from M. edulis and M. galloprovincialis, whereas the best performing allele model (BM101A) did the best at discriminating M. galloprovincialis from M. edulis and M. trossulus. Among the local environmental variables, salinity, water temperature, ice cover and chlorophyll a concentration were by far the greatest predictors, but their predictive performance varied among different allele models. In most cases changes in the allele frequencies along these environmental gradients were abrupt and occurred at a very narrow range of environmental variables. In general, regions of change in allele frequencies for M. trossulus occurred at 8–11 psu, 0–10 °C, 60%–70% of ice cover and 0–2 mg m−3 of chlorophyll a, M. edulis at 8–11 and 30–35 psu, 10–14 °C and 60%–70% of ice cover and for M. galloprovincialis at 30–35 psu, 14–20 °C.

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Different responses to environmental factors in terpene composition of Pinus heldreichii and P. peuce: Ecological and chemotaxonomic considerations

Archives of Biological Sciences ◽

10.2298/abs190705045r ◽

2019 ◽

Vol 71 (4) ◽

pp. 629-637

Author(s):

Nemanja Rajcevic ◽

Biljana Nikolic ◽

Petar Marin

Keyword(s):

Environmental Factors ◽

Endemic Species ◽

Environmental Conditions ◽

Natural Populations ◽

Balkan Peninsula ◽

Substrate Type ◽

Needle Anatomy ◽

Germacrene D ◽

Mixed Populations ◽

Geological Substrate

Many studies show the influence of the environment on terpene composition, but not many of them deal with the terpene composition variability in correlation with environmental factors in Pinus. We chose two endemic species ? P. heldreichii Christ. (Bosnian pine) and P. peuce Griseb. (Macedonian pine) ? two relict and (sub)endemic species of the Balkan peninsula. They mainly form pure stands but can appear in mixed populations, most commonly with each other. These species belong to different subgenera and thus differ greatly, especially in needle anatomy. ?-pinene, limonene and germacrene D predominated in Bosnian pine leaf oleoresins, while Macedonian pine oleoresin contained high amounts of ?-pinene. Furthermore, there were three chemotypes present in Bosnian, and only one in Macedonian pine. Oleoresins of Bosnian pine did not show correlation with climate, however, its composition changed in response to geological substrate type. Macedonian pine oleoresin showed a high correlation with the climate but changed only a little in response to geological substrate type. The oleoresin profiles showed strong species-dependent composition and variability. However, since each species expressed different responses to tested environmental conditions, it is important to take into consideration these variables when analyzing natural populations of the species.

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Environmental and spatial factors affect the composition and morphology of tadpole assemblages

Canadian Journal of Zoology ◽

10.1139/cjz-2017-0313 ◽

2018 ◽

Vol 96 (10) ◽

pp. 1130-1136

Author(s):

N.C.S. Marques ◽

F. Nomura

Keyword(s):

Environmental Factors ◽

Morphological Variation ◽

Environmental Conditions ◽

Environmental Variables ◽

Morphological Diversity ◽

Oviposition Site ◽

Spatial Factors ◽

Assemblage Composition ◽

Different Types ◽

Spatial Coordinates

Understanding how community compositions are affected by environmental and spatial factors are essential to provide knowledge about the distributions of species. Furthermore, these factors can play a role in species morphological variation. Tadpoles can be found in different types of aquatic microhabitats, showing a considerable amount of morphological diversity. We hypothesized that tadpole morphological diversity is controlled by ecological and spatial factors other than assemblage attributes, and that tadpole assemblage composition is affected by spatial factors. To test these hypotheses, we recorded the abundance of tadpoles from different ponds, identified eight environmental variables that represented local and landscape descriptors of the ponds, recorded the spatial coordinates of the ponds, and measured the morphological variation of assemblages. Spatial factors significantly affected the composition of tadpole assemblages, while both spatial and environmental factors affected morphological variation. The ability of tadpoles to alter their morphology in response to environmental factors might be a result of poor oviposition site choice, and this probably interacts with spatial factors to control the assemblage composition of tadpoles. Morphological variation is advantageous for tadpoles because it allows them to adjust their morphology to environmental conditions. This study has demonstrated how factors that control the assemblage composition of tadpoles also drive their morphological diversity.

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Environmental variables and errors in the preparation and administration of medicines

Revista Brasileira de Enfermagem ◽

10.1590/0034-7167-2016-0041 ◽

2018 ◽

Vol 71 (3) ◽

pp. 1046-1054 ◽

Cited By ~ 1

Author(s):

Francisco Gilberto Fernandes Pereira ◽

Márcia Barroso Camilo de Ataíde ◽

Ricardo Leal Silva ◽

Eugenie Desirèe Rabelo Néri ◽

Gerdane Celene Nunes Carvalho ◽

...

Keyword(s):

Environmental Factors ◽

Medication Errors ◽

Environmental Conditions ◽

Environmental Variables ◽

Physical Space ◽

Cross Sectional Study ◽

Hospital Environment ◽

Sectional Study ◽

Cross Sectional ◽

The Relationship

ABSTRACT Objective: to identify the relationship between environmental factors and errors in the preparation and administration of antibacterial. Method: an observational, cross-sectional study conducted between August and December, 2014 in two clinical units. The sample consisted of 265 doses of medication, observed in different shifts that through a form had the environmental conditions of noise, illumination, humidity, temperature and physical space measured in the preparation and administration stages. Results: the physical dimension for the preparation was inadequate in one unit (3.8m2), and the items illumination, temperature and noise were extremely oscillating in the three shifts and in the two clinics, with averages generally higher than the recommended for the hospital environment, however, variations in illumination and noise were not statistically significant to cause dose errors or erroneous medicine choice (p> 0.05). Conclusion: the environmental variables analyzed may favor medication errors in both the preparation and administration stages.

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Assessing alpha and beta diversities of benthic macroinvertebrates and their environmental drivers between watersheds with different levels of habitat transformation in Japan

Marine and Freshwater Research ◽

10.1071/mf18031 ◽

2019 ◽

Vol 70 (4) ◽

pp. 504 ◽

Cited By ~ 1

Author(s):

Chia-Ying Ko ◽

Tomoya Iwata ◽

Jun-Yi Lee ◽

Aya Murakami ◽

Junichi Okano ◽

...

Keyword(s):

Chlorophyll A ◽

Benthic Macroinvertebrates ◽

Environmental Variables ◽

Species Turnover ◽

Alpha Diversity ◽

Freshwater Ecosystems ◽

Environmental Drivers ◽

Habitat Transformation ◽

Β Diversity ◽

Different Levels

Little is known about differences in species diversity among ecological communities subject to different levels of human-caused habitat transformation and how this disturbance contributes to diversity through symbiotic dependencies with the environment in freshwater ecosystems. We estimated α and β diversities of benthic macroinvertebrates and relationships between diversity and environmental variables in Ado River (natural) and Yasu River (intermediately disturbed) watersheds, Japan. Alpha diversity was consistently slightly higher in the natural river watershed than in the intermediately disturbed one, but the spatial distribution was not equivalent. The opposite pattern was found for β diversity. Significant differences in environmental variables existed between the two river watersheds, with especially high chlorophyll-a concentrations detected in the intermediately disturbed watershed. Alpha diversity was not correlated with specific environmental variables, whereas water temperature and chlorophyll-a concentrations were the two most significant environmental variables influencing β diversity across sites in the two watersheds. These results suggest that diversity patterns in freshwater benthic macroinvertebrates are differentially influenced by levels of human-caused habitat transformation, especially that intermediately disturbed habitats may benefit species turnover, and further understanding how they relate to environmental variables is essential for protecting local to regional diversity and can provide useful information for conservation planning to maximise biodiversity at the watershed scale.

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Faculty Opinions recommendation of FREQ-Seq: a rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718014192.793477636 ◽

2013 ◽

Author(s):

Andreas Wagner ◽

Kathleen Sprouffske

Keyword(s):

Cost Effective ◽

Allele Frequencies ◽

Mixed Populations

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Allele frequencies of single nucleotide polymorphisms of clinically important drug-metabolizing enzymes CYP2C9, CYP2C19, and CYP3A4 in a Thai population

Scientific Reports ◽

10.1038/s41598-021-90969-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Rattanaporn Sukprasong ◽

Sumonrat Chuwongwattana ◽

Napatrupron Koomdee ◽

Thawinee Jantararoungtong ◽

Santirhat Prommas ◽

...

Keyword(s):

Snp Genotyping ◽

Allele Frequencies ◽

Nucleotide Polymorphisms ◽

Poor Metabolizer ◽

Thai Population ◽

Metabolizing Enzymes ◽

Single Nucleotide ◽

Genotyping Assay ◽

Intermediate Metabolizer ◽

Important Drug

AbstractPrior knowledge of allele frequencies of cytochrome P450 polymorphisms in a population is crucial for the revision and optimization of existing medication choices and doses. In the current study, the frequency of the CYP2C9*2, CYP2C9*3, CYP2C19*2, CYP2C19*3, CYP2C19*6, CYP2C19*17, and CYP3A4 (rs4646437) alleles in a Thai population across different regions of Thailand was examined. Tests for polymorphisms of CYP2C9 and CYP3A4 were performed using TaqMan SNP genotyping assay and CYP2C19 was performed using two different methods; TaqMan SNP genotyping assay and Luminex x Tag V3. The blood samples were collected from 1205 unrelated healthy individuals across different regions within Thailand. Polymorphisms of CYP2C9 and CYP2C19 were transformed into phenotypes, which included normal metabolizer (NM), intermediate metabolizer (IM), poor metabolizer (PM), and rapid metabolizers (RM). The CYP2C9 allele frequencies among the Thai population were 0.08% and 5.27% for the CYP2C9*2 and CYP2C9*3 alleles, respectively. The CYP2C19 allele frequencies among the Thai population were 25.60%, 2.50%, 0.10%, and 1.80% for the CYP2C19*2, CYP2C19*3, CYP2C19*6, and CYP2C19*17 alleles, respectively. The allele frequency of the CYP3A4 (rs4646437) variant allele was 28.50% in the Thai population. The frequency of the CYP2C9*3 allele was significantly lower among the Northern Thai population (P < 0.001). The frequency of the CYP2C19*17 allele was significantly higher in the Southern Thai population (P < 0.001). Our results may provide an understanding of the ethnic differences in drug responses and support for the utilization of pharmacogenomics testing in clinical practice.

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Regional environmental controllers influence continental scale soil carbon stocks and future carbon dynamics

Scientific Reports ◽

10.1038/s41598-021-85992-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Daniel Ruiz Potma Gonçalves ◽

Umakant Mishra ◽

Skye Wills ◽

Sagar Gautam

Keyword(s):

Environmental Factors ◽

Land Cover ◽

Environmental Conditions ◽

Climate Feedback ◽

Soil Types ◽

Climatic Data ◽

Earth System ◽

Land Cover Types ◽

Continental Scale ◽

Soc Stocks

AbstractUnderstanding the influence of environmental factors on soil organic carbon (SOC) is critical for quantifying and reducing the uncertainty in carbon climate feedback projections under changing environmental conditions. We explored the effect of climatic variables, land cover types, topographic attributes, soil types and bedrock geology on SOC stocks of top 1 m depth across conterminous United States (US) ecoregions. Using 4559 soil profile observations and high-resolution data of environmental factors, we identified dominant environmental controllers of SOC stocks in 21 US ecoregions using geographically weighted regression. We used projected climatic data of SSP126 and SSP585 scenarios from GFDL-ESM 4 Earth System Model of Coupled Model Intercomparison Project phase 6 to predict SOC stock changes across continental US between 2030 and 2100. Both baseline and predicted changes in SOC stocks were compared with SOC stocks represented in GFDL-ESM4 projections. Among 56 environmental predictors, we found 12 as dominant controllers across all ecoregions. The adjusted geospatial model with the 12 environmental controllers showed an R2 of 0.48 in testing dataset. Higher precipitation and lower temperatures were associated with higher levels of SOC stocks in majority of ecoregions. Changes in land cover types (vegetation properties) was important in drier ecosystem as North American deserts, whereas soil types and topography were more important in American prairies. Wetlands of the Everglades was highly sensitive to projected temperature changes. The SOC stocks did not change under SSP126 until 2100, however SOC stocks decreased up to 21% under SSP585. Our results, based on environmental controllers of SOC stocks, help to predict impacts of changing environmental conditions on SOC stocks more reliably and may reduce uncertainties found in both, geospatial and Earth System Models. In addition, the description of different environmental controllers for US ecoregions can help to describe the scope and importance of global and local models.

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The influence of dynamic environmental interactions on detection efficiency of acoustic transmitters in a large, deep, freshwater lake

Animal Biotelemetry ◽

10.1186/s40317-019-0179-1 ◽

2019 ◽

Vol 7 (1) ◽

Cited By ~ 3

Author(s):

Natalie V. Klinard ◽

Edmund A. Halfyard ◽

Jordan K. Matley ◽

Aaron T. Fisk ◽

Timothy B. Johnson

Keyword(s):

Study Design ◽

Environmental Conditions ◽

Power Output ◽

Environmental Variables ◽

Acoustic Telemetry ◽

Detection Efficiency ◽

Data Interpretation ◽

Heterogeneous Environments ◽

Depth Range ◽

Dynamic Relationship

Abstract Background Acoustic telemetry is an increasingly common method used to address ecological questions about the movement, behaviour, and survival of freshwater and marine organisms. The variable performance of acoustic telemetry equipment and ability of receivers to detect signals from transmitters have been well studied in marine and coral reef environments to inform study design and improve data interpretation. Despite the growing use of acoustic telemetry in large, deep, freshwater systems, detection efficiency and range, particularly in relation to environmental variation, are poorly understood. We used an array of 90 69-kHz acoustic receivers and 8 sentinel range transmitters of varying power output deployed at different depths and locations approximately 100–9500 m apart for 215 days to evaluate how the detection efficiency of acoustic receivers varied spatially and temporally in relation to environmental conditions. Results The maximum distance that tags were detected ranged from 5.9 to 9.3 km. Shallow tags consistently had lower detection efficiency than deep tags of the same power output and detection efficiency declined through the winter months (December–February) of the study. In addition to the distance between tag and receiver, thermocline strength, surface water velocity, ice thickness, water temperature, depth range between tag and receiver, and number of fish detections contributed to explaining variation in detection efficiency throughout the study period. Furthermore, the most significant models incorporated interactions between several environmental variables and tag–receiver distance, demonstrating the complex temporal and spatial relationships that exist in heterogeneous environments. Conclusions Relying on individual environmental variables in isolation to interpret receiver performance, and thus animal behaviour, may be erroneous when detection efficiency varies across distances, depths, or tag types. As acoustic telemetry becomes more widely used to study ecology and inform management, it is crucial to understand its limitations in heterogeneous environments, such as freshwater lakes, to improve the quality and interpretation of data. We recommend that in situ range testing and retrospective analysis of detection efficiency be incorporated into study design for telemetry projects. Furthermore, we caution against oversimplifying the dynamic relationship between detection efficiency and environmental conditions for the sake of producing a correction that can be applied directly to detection data of tagged animals when the intended correction may not be justified.

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Impacts of Environmental Factors on Head and Neck Cancer Pathogenesis and Progression

Cells ◽

10.3390/cells10020389 ◽

2021 ◽

Vol 10 (2) ◽

pp. 389

Author(s):

Marisol Miranda-Galvis ◽

Reid Loveless ◽

Luiz Paulo Kowalski ◽

Yong Teng

Keyword(s):

Head And Neck Cancer ◽

Environmental Factors ◽

Head And Neck ◽

Neck Cancer ◽

Molecular Mechanisms ◽

Metastatic Cancer ◽

Environmental Drivers ◽

Cancer Pathogenesis ◽

Gene Environment ◽

The Impact

Epidemiological and clinical studies over the past two decades have provided strong evidence that genetic elements interacting with environmental components can individually and collectively influence one’s susceptibility to cancer. In addition to tumorigenic properties, numerous environmental factors, such as nutrition, chemical carcinogens, and tobacco/alcohol consumption, possess pro-invasive and pro-metastatic cancer features. In contrast to traditional cancer treatment, modern therapeutics not only take into account an individual’s genetic makeup but also consider gene–environment interactions. The current review sharpens the focus by elaborating on the impact that environmental factors have on the pathogenesis and progression of head and neck cancer and the underlying molecular mechanisms involved. Recent advances, challenges, and future perspectives in this area of research are also discussed. Inhibiting key environmental drivers of tumor progression should yield survival benefits for patients at any stage of head and neck cancer.

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